The activating missense membrane-proximal mutation in CSF3R (p.T618I) has been reported to occur in approximately 83% of cases of chronic neutrophilic leukemia; some reports indicate this mutation may be present in cases of atypical chronic myeloid leukemia as well. The CS3R T618I mutation has been associated with response to JAK2 inhibitors but not dasatinib. A germline activating CSF3R mutation (p. T617N) has been described in autosomal dominant hereditary neutrophilia associated with splenomegaly and increased circulating CD34-positive myeloid progenitors. Nonsense and/or frameshift somatic mutations truncating the cytoplasmic domain of CSF3R have been described in approximately 40% of patients with severe congenital neutropenia and in the context of mutations in other genes may be associated with progression to acute myeloid leukemia. These activating truncating mutations have also been found in patients with chronic neutrophilic leukemia or atypical chronic myeloid leukemia. Some of these cytoplasmic truncating mutations have been associated with responses to dasatinib but not JAK2 inhibitors.
MPL encodes the thrombopoietin receptor, an important growth and survival factor for megakaryocytes. Somatic activating mutation in MPL (W515L, W515K) has been reported in approximately 1%-10% of cases of JAK2 V617F-negative myelofibrosis, essential thrombocythemia, a subset of cases of acute megakaryoblastic leukemia and has been associated with sensitivity to JAK inhibitors. The W515 mutations are typically not observed in polycythemia vera or other myeloid disorders (chronic myelomonocytic leukemia, myelodysplastic syndrome). A S505N activating mutation has also been described in familial essential thrombocythemia. MPL mutation is included as one of the major diagnostic criteria for primary myelofibrosis and essential thrombocythemia in the 2016 revision of the WHO classification.
Activating mutations in JAK1 (SH2-, pseudokinase -and kinase- domains) have been reported in approximately 5-20% of cases of T-Cell Acute Lymphoblastic Leukemia, in "Ph-like ALL" and in less than 5% of Acute Myeloid Leukemia. Some, but not all, of these mutations have been shown to be inhibitable by ATP-competitive JAK inhibitors or Type I interferon.
NRAS encodes a membrane protein GTPase that is a central mediator of downstream growth factor receptor signaling, critical for cell proliferation and survival. Mutations in codons 12, 13, and 61 of NRAS have been reported in 7-22% of acute myeloid leukemia, 12% of chronic myelomonocytic leukemia, 20% of blastic plasmacytoid dendritic cell neoplasm, 16% of juvenile myelomonocytic leukemia, 4-10% of myelodysplastic syndromes, and 5% of primary myelofibrosis. In addition, NRAS mutations have been described in approximately 15% of cases of B-ALL and, interestingly, some cases of ALL may show more than one abnormality in the RAS pathway. NRAS mutations are associated with an unfavorable prognosis in chronic myelomonocytic leukemia and primary myelofibrosis. NRAS mutations are also associated with an unfavorable prognosis in myelodysplastic syndrome, particularly in patients predicted to have lower-risk myelodysplastic syndrome (NCCN Guidelines for Myelodysplastic Syndromes). NRAS mutations do not seem to have significant prognostic impact in AML.
NOTCH2 gain of function mutations have been reported in apprximately 25% of splenic marginal zone lymphomas and are thought to be rare in non-splenic marginal zone lymphomas. These mutations are typically located near the C-terminal PEST domain and lead to protein truncation or, more rarely, are nonsynonymous substitution mutations affected the extracellular heterodimerization domain. NOTCH2 mutations may be associated with a worse prognosis among cases of splenic marginal zone lymphoma. In addition, NOTCH2 PEST domain mutations have been reported in approximately 8% of diffuse large B cell lymphomas and in vitro systems have demonstrated these PEST domain mutant NOTCH2 receptors have increased activity compared to wild type NOTCH2. In addion, copy number gain has been reported in a subset of DLBCL cases with NOTCH2 mutations.
Ras-like-without-CAAX-1 (RIT1) gene is a member of the RAS gene family. Recurrent somatic mutations of RIT1 have been reported in approximately 7% of cases of chronic myelomonocytic leukemia, and less than 5% of cases of myelodysplastic syndrome and less than 5% of acute myeloid leukemia. The mutations typically occur in the Switch II effector domain, and the affected residues are close to codon Q79, which is analogous to amino acid Q61 of NRAS or KRAS where mutations frequently occur in cancer. Moreover, the experimental Q79L mutation in RIT1 has been reported to confer constitutive activation of the protein. RIT1 mutations are typically mutually exclusive of mutations in other RAS family members. In addition, RIT1 maps to the minimal common amplified region (1q21-22) in 1q gains frequently found in other cancers. 1q amplification involving the RIT1 locus has been reported in 4-18% of cases of myelofibrosis as well as less than 5% of chronic myelomonocytic leukemia, less than 5% of myelodysplastic syndromes and less than 5% of acute myeloid luekemia. In rare cases mutations and amplifcations of RIT1 may coexist. In general, RIT1 has been reported to increased phosphorylation of AKT and activate proliferation through the mitogen activated protein kinase pathway.
DNMT3A is a DNA methyltransferase. Recurrent, somatic, heterozygous mutations in DNMT3A have been reported in approximately 18-25% of cases of acute myeloid leukemia (up to 34% of normal karyotype AML), 12-18% of cases of myelodysplastic syndrome, up to 15% of myeloproliferative neoplasms, less than 5% of cases of chronic myelomonocytic leukemia and 15% of cases of adult, eary T cell precursor acute lymphoblastic leukemia. DNMT3A is also one of the most frequently mutated genes in CHIP and CCUS. Mutations in DNMT3A may occur together with mutations in other genes including JAK2, FLT3, IDH1/IDH2, ASXL1, TET2 and NPM1. DNMT3A mutations have been associated with reduced enzymatic activity or altered histone binding, as well as reduced DNA methylation in various genomic regions and altered gene expression in some models. Codon R882 is a hotspot for mutations in DNMT3A. DNMT3A mutations may be associated with adverse prognosis in specific subtypes of AML according to some, but not all studies; the prognostic significance of DNMT3A in AML may depend on patient age, type of DNMT3A mutation (R882 or non-R882 mutation) and the co-existence (or absence) of specific mutations in other genes. DNMT3A mutations may also be associated with adverse prognosis in MDS according to some studies.
Fanconi anemia is a rare genetic syndrome characterized by developmental defects, bone marrow failure and increased cancer risk. A diagnosis of Fanconi Anemia usually requires detection of a pathogenic mutation in a Fanconi Anemia gene and/or a positive chromosomal breakage test. A variety of different inactivating mutations in FANCL have been described in a small subset of patients with Fanconi Anemia and patients with myeldodysplastic syndrome(less than 5%). Pathogenic mutations are often found in homozygous or compound heterozygous state. In addition, pathogenic variants in introns have been described that are not detected by this test.
The nuclear export protein, XPO1, is mutated in less than 5% of cases of chronic lymphocytic leukemia (CLL). Most frequently these mutations affect codon Glu571. Cases of CLL with mutations in XPO1 tend to be associated with a higher prevalence of CD38 expression (>30% of tumor cells), ZAP70 expression (> 20% of tumor cells), concomitnat NOTCH1 mutation and unmutated IGHV. Given the low prevalence of XPO1 mutations, prognostic signficance has not been firmly establlished. XPO1 has been successfully targeted in some experimental models of CLL.
CXCR4 is a chemokine receptor which has been shown to mutated in approximately 25-30% of patients with Waldenstrom's Macroglobulinemia(WM). The mutations are nonsense and frameshift mutations in the carboxy terminus of the protein. Similar mutations are found in WHIM (Warts, Hypogammaglobulinemia, Infection and Myelokathexis) syndrome, a rare, autsomal dominant genetic disorder. These mutations in the carboxy terminal tail lead to impaired receptor desensitization and internalization, resulting in enhanced receptor activation and increased expression. Almost all WM patients with mutation of CXCR4 also carry the MYD88 L265P mutation. Mutations in CXCR4 appear to be mutually exclusive of mutations in CD79A/CD79B. Patients with CXCR4 mutations may be candidates for targeted therapy since CXCR4 antagonists have been used in patients with WHIM syndrome. The presence of CXCR4 mutations may affect response to Ibrutinib therapy according to some studies.
SF3B1 encodes a core component of the U2 small nuclear ribonucleoprotein, involved in the recognition of the branchpoint sequence during RNA splicing. SF3B1 is one of several genes involved in RNA splicing that has been identified as recurrently mutated in MDS and other malignancies. SF3B1 is the most commonly mutated gene found in MDS (20-33% of MDS overall). SF3B1 mutations are highly associated with subtypes of MDS characterized by ring sideroblasts (MDS with ring sideroblasts and MDS with multilineage dysplasia and ring sideroblasts), present in ~80% of these patients. In addition, many cases (60-80%) of myelodysplastic/myeloproliferative neoplasm with ring sideroblast and thrombocytosis (MDS/MPN-RS-T) harbor SF3B1 mutations. SF3B1 mutations are also found in 12% of blastic plasmacytoid dendritic cell neoplasm, 4-7% of primary myelofibrosis, 5% of CMML, less than 5% of de novo AML and less than 5% of essential thrombocythemia and polycythemia vera. SF3B1 mutations tend to occur in exons 13-16 and appear to be enriched at codons Lys700, Lys666, His662, Arg625 and Glu622. Missense mutations have been reported in approximately 5-10% of cases of chronic lymphocytic leukemia (CLL) and are reported to be associated with del11q , unmutated IGHV and may predict an adverse prognosis in CLL. Mutations in splicing factor components are usually mutually exclusive. Among cases of CLL, SF3B1 mutations tend to be exclusive of NOTCH1 mutations according to one study. The presence of SF3B1 mutation has been included in the diagnostic criteria for MDS/MPN-RS-T and MDS-RS diagnosis in the 2016 revision of the WHO classification. SF3B1 mutations are independently associated with a more favorable prognosis in MDS (NCCN Guidelines for Myelodysplastic Syndromes) and are highly predictive for the presence of ring sideroblasts. SF3B1 mutations are also reported to be highly specific for secondary acute myeloid leukemia, and may also be helpful in identifying a subset of therapy-related AML or elderly patients with de novo acute myeloid leukemia with worse clinical outcomes. SF3B1 mutations are associated with an unfavorable prognosis in essential thrombocythemia. SF3B1 has a critical role in MDS by affecting the expression and splicing of genes involved in specific cellular processes/pathways, many of which are relevant to the known MDS-RS pathophysiology, suggesting a causal link.
IDH1 is an enzyme localized to the cytoplasm and peroxisomes and involved in citrate metabolism. Mutations at Arg132 of IDH1 are typically heterozygous mutations and considered gain of function mutations that lead to increased levels of 2-hydroxyglutarate which are believed to alter epigenetic regulation (ie, DNA methylation) in AML. Mutations of IDH1 appear to be mutually exclusive of mutations in TET2, another gene involved in regulation of DNA methylation, and also exclusive of mutations in IDH2. Mutations of IDH1 have been shown to lead to increased DNA methylation in AML. Recurrent missense mutation of Arg 132 in IDH1 has been reported in approximately 5-15% of cases of acute myeloid leukemia and is often associated with a normal karyotype, wild type CEBPA, wild type FLT3 and the presence of NPM1 mutations. In addition, this mutation has been reported in approximately 10-20% of cases with leukemic transformation of myeloproliferative neoplasms and has been reported in less than 5% of chronic phase primary myelofibrosis, less than 5% of myelodysplastic syndrome and rare cases of polycythemia vera, essential thrombocytosis and chronic myelomonocytic leukemia. The prognostic impact of IDH1 mutations in AML appears uncertain, however, in the settings of primary myelofibrosis and polycythemia vera, the presence of IDH1 mutation is independently associated with inferior survival. Mutant IDH1 represents a therapeutic target in some clinical settings.
Copy number loss of in IKZF2 (HELIOS) have been described in approximately 50-60% of low haploid acute lymphoblastic leukemia. Occasional inactivating mutations of IKZF2 have also been described. IKZF2 and Ras pathway alterations are usually mutually exclisive according to one report. In some experimental models, higher amounts of pERK and pS6 were observed after knockdown of Ikzf2 in cell lines. This raises the possibility that IKZF2 is a modulator of Ras and PI3K signaling and the efficacy of therapeutic targeting of PI3K and mTOR in such cases remains to be determined.
MYD88 is an adaptor protein in the Toll-like receptor and interleukin 1 receptor pathway which mediates activation of NF-KB. The somatic, activating mutation in MYD88 (p.L265P) has been reported in approximately 90% of lymphoplasmacytic lymphoma (Waldenostrom's macroglobuinemia), 20-30% of cases of diffuse large B cell lymphoma (DLBCL), 10-60% of IgM MGUS, 10% of MALT lymphoma and up to 10% of chronic lymphocytic leukemia. It has not been reported in acute leukemia or multiple myeloma (including IgM myeloma). The L265P mutation increases in NFkB activity, JAK-STAT3 (Janus kinase-signal transducer and activator of transcription 3) signalling and interferon-b production. Targetted therapy using inhibitors of the different components of this pathway are at various stages of investigation. Responses to targeted therapy with Ibrutinib may vary according to MYD88 and CXCR4 mutation status according to some studies.
Beta catenin is a transcriptional co-regulator and an adapter protein for cellular adhesion; it comprises part of the Wnt signaling pathway and intracellular levels of beta-catenin are regulated by its phosphorylation, ubiquitination and proteosomal degradation. Accumulation of nuclear beta catenin can lead to a tumoral phenotype and oncogenic transformation in a variety of solid tumors. Various oncogenic mutants of beta catenin have been found in different tumor types which alter its degradation, leading to its accumulation and promoting tumor growth. Some of these mutations are located at the N-terminus of the protein at the sites of phosphorylation which normally regulate its degradation. Interestingly, in a recent study, 38% of patients with myelodysplastic syndromes or acute myeloid leukaemia, showed increased β-catenin signalling and nuclear accumulation of beta catenin in osteoblasts was associated with increased Notch signalling in haematopoietic cells consistent with a model where abnormalities of osteolineage cells are associated with myeloid malignancies. In addition, aberrant Wnt siganling has been reported to play a role in chronic myeloid leukemia, acute lymphoblastic leukemia and non-hodgkin lymphomas. Inhibition of beta catenin using small molecule inhibitors is currently being investigated in various tumor types. Recent studies suggest that targeting of the Wnt pathway and beta catenin may be promising targets in the therapy of acute myeloid leukemia.
SETD2 encodes a H3K36 trimethylase and loss of function mutations (missense, nonsense and frameshift mutations) have been reported in approximately 10% of acute myeloid leukemia, and 10% of acute lymphoblastic leukemia, including acute early T cell precursor acute lymphoblastic leukemia. SETD2 mutations appear to be enriched among cases of acute leukemia with rearrangements of MLL. Coexistence of two mutations in SETD2 has been described and together with recurrent loss of function mutations suggest this gene is acts as a tumor suppressor. The presence of loss of function mutations in SETD2 has been associated with global loss of H3K36me3. In addition, the presence of SETD2 mutations may be associated with therapy resistance.
Casitas B lineage lymphoma b (CBL-B) belongs to the single-protein RING family of ubiquitin ligases. CBLB mutations have been reported in accelerated phase and blast phase chronic myelogenous leukemia but not chronic phase of chronic myelogenous leukemia. CBLB mutations have been reported together with TET2 mutations in some cases. CBLB mutations have not been reported in childhood acute lymphoblastic leukemia according to one study.
GATA2 is a member of the GATA transcription factors which play a role in hematopoiesis. GATA2 mutations in the zinc finger domains have been described in accelerated phase and blasts phase chronic myelogenous leukemia as well as 5-10% of acute myeloid leukemia and familial syndromes with a predisposition to acute myeloid leukemia and myelodysplastic syndromes. Co-existing mutations in ASXL1 have been reported in a subset of patients with mutations in GATA2 and are believed to represent an important step in myeloid transformation, particularly to chronic myelomonocytic leukemia in young female patients. Other reports suggest that in cases of AML, GATA2 mutations have a higher prevalence among cases with biallelic CEBPA mutations and were not observed in cases with monoallelic CEBPA mutations. In general, the GATA2 pathogenic mutations are loss-of-function mutations (nonsense, frameshift, splice site mutations or missense mutations(codons 349-398)) and are believed to result in impairment of granulocyte differentiation. In MDS, GATA2 mutations may be associated with a poor prognosis. If clinical findings and family history are concerning for an inherited disorder, then genetic counseling may be helpful, if clinically indicated.
PIK3CA is the the p110 catalytic subunit-alpha of phosphatidylinositol 3 kinase. Activating mutations of PIK3CA occur in various types. PIK3CA mutations have been reported in approximately 8% of cases of diffuse large B cell lymphoma and are typically mutually exclusive of PTEN loss in that tumor type. PIK3CA mutations are very rare in chronic lymphocytic leukemia and believed to be absent in acute myeloid leukemia and myelodysplastic syndromes. PIK3CA mutations are potentially targetable in some settings and pathway inhibitors are currently under investigation .
WHSC1 (also known as NSD2 or MMSET) is a H3K36 methyltransferase that converts unmodified H3K36 to the monomethylated and dimethylated forms. NSD2 was recently found to show clonal and subclonal p.E1099K or p.D1125N activating alterations in 15% of t(12;21) ETV6-RUNX1–containing and 15% of TCF3-PBX1 contaning pediatric B-ALLs. The p.E1099K mutation appears to be less prevalent in other types of B-ALL(less than 5%) and both mutations appear to be absent in T-ALL, pediatric AML and adult ALL. In experimental models, increased H3K36 dimethylation and decreased unmodified H3K36 was associated with the NSD2 p.E1099K variant or the t(4;14) translocation( which leads to overexpression of NSD2). Overexpression of NSD2 in t(4;14)-positive multiple myeloma (MM) is also associated with globally increased levels of H3K36 dimethylation and decreased K27 trimethylation. NSD2 is considered to be a potential therapeutic target for a subset of cases of pediatric B-ALL.
Rearrangements of PDGFRA (including FIP1L1-PDGFRα) is a common abnormality among patients with chronic eosinophilic leukemia. In addition, activating mutations (eg, p.H650Q, p. N659S, p.R748G, p.Y849S) in PDGFRA have been reported in FIP1L1-PDGFRα-negative chronic eosinophilic leukemia and resistance mutations in PDGFRA (eg. p.D842V, p.T674I) have been reported in the setting of imatinib therapy for patients with FIP1L1-PDGFRα. These PDGFRA mutations have variable responses to the different available tyrosine kinase inhibitors.
KIT(cKIT) mutations are present in approximately 8-25% of cases of acute myeloid leukemia and have a higher prevalence in the favorable cytogenetic risk group including core binding factor (CBF) AMLs (ie, (t(8;21)(q22;q22)(RUNX1-RUNX1T1), inv(16)(p13q22)(CBFB-MYH11)) or normal karyotype AML. Mutations of KIT in AML are most common in KIT exon 17 (within the activation loop of the tyrosine kinase domain) but may also occur in KIT exons 8 (extracellular portion of the receptor implicated in dimerization), 9-11 (juxtamembrane/transmembrane domains). The presence of KIT mutations has been reported to be associated with a poorer survival and/or higher risk of relapse than expected for patients with the t(8;21)(q22;q22)(RUNX1-RUNX1T1), and to a lesser extent, in inv(16) AML. KIT mutations are also important in systemic mastocytosis and various mast cell disorders; over 90% of cases of systemic mastocytosis carry mutations in exon 17 of KIT (most commonly D816V or rarely D816H, D816Y or other variants). In patients with mastocytosis, the KIT mutations may be detectable in non-mast cell hematopoietic cells. The KIT D816V mutation has been shown to be resistant to imatinib; other KIT mutations may show variable responses to imatinib. The KIT D816V mutant has been reported to be sensitive to other tyrosine kinase inhibitors. In the context of core binding factor AMLs, the KIT mutation status can help direct therapeutic management.
Ten-Eleven Translocation-2 (TET2) encodes a dioxygenase that converts 5-methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (5-hmC) and promotes DNA demethylation. TET2 is a tumor suppressor gene and loss-of-function via mutations, deletion and IDH1/2 (Isocitrate Dehydrogenase 1 and 2) gene mutations is a common event in myeloid and lymphoid malignancies. TET2 is also present in about 10% of otherwise healthy elderly individuals with clonal hematopoiesis of indeterminate potential (CHIP) and in some patients with unexplained cytopenia but who do not satisfy diagnostic criteria for MDS, so-called clonal cytopenia with undetermined significance (CCUS). Mutations in TET2 occur in 50-60% of chronic myelomonocytic leukemias. Comutation of TET2 and SRSF2 was highly predictive of a myeloid neoplasm characterized by myelodysplasia and monocytosis, including but not limited to, chronic myelomonocytic leukemia. TET2 mutations are also found in 20-40% of systemic mastocytosis, 36% of blastic plasamcytoid dendritic cell neoplasm, 12-32% of acute myeloid leukemia, 10-20% of primary myelofibrosis, 10-33% of myelodysplastic syndromes, 10% of myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T), 22% of polycythemia vera, and 16% of essential thrombocythemia. TET2 mutations are absent in juvenile myelomonocytic leukemia and show a low prevalence (less than 5%) in pediatric AML. Among lymphoid neoplasms, TET2 mutations are reported in approximately 30% of angioimmunoblastic lymphomas and less than 15 % of other mature T cell lymphomas and mature B cell lymphomas. In general, the mutations in TET2 are typically loss of function variants (frameshift, missense, nonsense mutations) that may be monoallelic or biallelic and occur throughout the gene. TET2 mutations tend to be mutually exclusive of mutations in IDH1/IDH2. TET2 mutations are associated with unfavorable outcomes and shorter survival after hematopoietic stem cell transplantation in patients with myelodysplastic syndrome (PMID: 25092778). In acute myeloid leukemia with wild-type FLT3-ITD and normal karyotype or intermediate-risk cytogenetic abnormalities, TET2 mutations are associated with an unfavorable prognosis.
FBXW7 is a ubiquitin protein ligase subunit which regulates levels of NOTCH, cyclin E, and other proteins. Loss-of-function mutations of FBXW7 lead to constitutive Notch1 pathway activation via inhibition of ubiquitin-mediated degradation of activated NOTCH1 and MYC. Mutations of FBXW7 include missense and frameshift mutations. FBXW7 have been reported in approximately 4-30% of cases of T-ALL less than 5% of cases of B-ALL, less than 5% of cases of CLL and appear to be very rare/absent in acute myeloid leukemia. According to some, but not all studies, NOTCH1 pathway activation by NOTCH1 mutations or FBXW7 mutations in TALL have been associated with an improved prognosis (in cases without concomitant RAS or PTEN mutations) compared to cases without mutations in NOTCH1 or FBXW7. FBXW7 mutations may occur alone or together with mutations in NOTCH1 (typically those in the heterodimerization domain and more rarely those in the PEST domain of NOTCH1). FBXW7 mutations may result in resistance to gamma secretase inhibitors according to some experimental studies.
Toll-like receptor (TLR) genes encode important components of innate immune system which is believed to play a role in the pathophysiology of myelodysplastic syndromes(MDS). Various TLR isoforms have been shown to be overexpressed in bone marrow CD34+ cells in MDS. In addition, the TLR2 p.F217S has been reported in approximately 10% of MDS patients. This variant is associated with enhanced activation of downstream signaling including NF-κB activity. TLR2 p.F217S may be associated with a higher frequency of chromosome 7 deletion in MDS as well. It is important to note that the TLR2 p.F217S variant has not been clearly established as a somatic variant and it is reported in the ESP database with an overall allele frequency of approximatly 0.3%. The potenital role of therapeutic targeting of TLR2 in MDS remains to be established.
IL7R (Interleukin 7 receptor alpha) is required for normal lymphocyte development. Loss of function mutations are seen in severe combined immunodeficiency. More recently, heterozygous, somatic, activating mutations have been described in pediatric B-cell and T-cell acute lymphoblastic leukemia. These mutations are most frequently in-frame insertions and deletions in the transmembrane domain. In general, these mutations lead to the addition of a cysteine residue in the juxtamembrane domain, a change that is essential for the resultant constiutive activation of the receptor and JAK/STAT and mTOR pathways. Recently, non-cysteine mutations have been described in the transmembrane domain of IL7R, some of which are activating. IL7R mutations have been described in up to 6% of childhood B-ALL and are typically associated with aberrant CRLF2 expresssion and in up to 10% of childhood T-ALL/adult T-ALL and may co-exist with NOTCH1 mutations. These mutations are rare in adult AML(1%). The prognostic significance of these mutations remains to be elucidated. These mutations may have implications for targetted therapy. In addition to in frame exon 6 in/dels, activating mutations in exon 5 have been described in IL7R which are not detected by this assay.
Mutations of CSF1R (M-CSF receptor) at codon 969 were initially reported in approximately 10-20% of cases of myelodsyplasia and acute myeloid leukemia including cases of chronic myelomonocytic leukemia and acute myeloid leukemia with monocytic differentiation. However, other studies have not been able to reproduce those findings. In addition to the Y969 mutation, other mutations in CSF1R as well as translocations involving CSF1R have been described in CSF1R. Interestingly, other mutations in CSF1R have also been reported to be associated with different disease, namely hereditary diffuse leukoenceophalopathy with spheroids.
Mutations of NPM1 have been reported in approximately 25-35% of cases of acute myeloid leukemia (AML). The mutations of NPM1 are frameshift mutations in the C-terminus of the protein that alter the C-terminal amino acid sequence and are associated with aberrant cytoplasmic localization of the protein. NPM1 mutations in AML are typically associated with a normal karyotype and may co-exist with FLT3 mutations. The presence of NPM1 mutations has been associated with improved complete remission rates, but not necessarily overall survival, in multivariate analysis including assessment of the variety of more recently discovered mutations that may be present in AML. In addition, cytogenetically normal AML with mutated NPM1, without FLT3 ITD or mutated DNMT3A, has been considered to be a favorable genetic risk group according to some studies, although other studies suggest that coexistant mutations in IDH1 or IDH2 may be required for the favorable risk effect of NPM1.
PIM1 is a member of the PIM family of proteins which are proto-oncogenes, serine-threonine kinases with increased expression in a variety of malignancies. PIM1 expression appears to be up-regulated by STAT5, and has been found to be over-expressed in primary AML blast samples. In particular, PIM1 has associated with FLT3 mediated leukemogenesis in FLT3-ITD AML. PIM1 expression was noted to be 25-fold higher than in FLT3-ITD samples, as compared to wild type FLT3 (WT) AML samples. The PIM kinases, therefore, represent potential therapeutic targets in AML, particularly in those cases harboring FLT3-ITD mutations. According to one study, the small molecule inhibitor of PIM1, AR00459339, alone and in combination with a FLT3 inhibitor (AR00454200), resulted in significant cytotoxicity in FLT3-ITD cell lines and patient samples that strikingly parallels the effects of FLT3 inhibition. A variety of mutations have been reported throughout PIM1 in various types of malignancy including hematopoietic tumors, but PIM1 mutations appear to be extremely rare in acute myeloid leukemia and myelodysplasia.
IKZF1(Ikaros) is a transcriptional regulator of B cell development and is believed to have tumor suppressor-like properties. Deletions (whole gene and/or partial gene deletions) of IKZF1 have been reported in approximately 15-28% of BCR-ABL1-Negative_B-cell ALL, 70-90% of BCR-ABL1-Positive B-cell ALL. IKZF1 mutations are also found in approximately 40% of "Ph-like" ALL. Loss of functions mutations (missense, nonsense, frameshift mutations) have also been reported in IKZF1 in ALL and appear to be much less common (less than 5% of cases) than deletions. Deletions and mutations in IKZF1 have been associated with adverse prognosis and greater risk of relapse.
CUX1(CUTL1, CDP) is a transcription factor proposed to act as a haploinsufficient myeloid tumor suppressor that maps to the commonly deleted segment in cases of myeloid malignancies with complete or partial loss of chromosome 7; such cases show reduced expression of CUX1. In addition, loss of function (missense, nonsense, frameshift) mutations of CUX1, occuring throughout the gene, have been described in a variety of cancer types; they occur in up to 10% of chronic myelomonocytic leukemia and are rare (less than 5%) in acute myeloid leukemia, myelodysplastic syndromes, myeloproliferative neoplasms and chronic lymphocytic leukemia. When loss of function mutations do occur in CUX1, they do not coexist with monosomy 7 or del7q, consistent with its role as a haploinsufficient tumor suppressor gene in most cases; nevertheless, compound heterozygous loss of function mutations in CUX1 have been described in rare cases. In MDS and MDS/MPN, both CUX1 inactivation and −7/del(7q) have been associated with poorer overall survival according to some studies. CUX1 deficiency has been reported to activate phosphoinositide 3-kinase (PI3K) signaling through direct transcriptional downregulation of the PI3K inhibitor PIK3IP1 (phosphoinositide-3-kinase interacting protein), leading to increased tumor growth and susceptibility to PI3K-AKT inhibition in some models.
LUC7L2 is thought to be an RNA binding protein and component of the RNA splicing machinery. Recent studies suggest that it may be a recurrent mutation in a subset of patients with AML and/or MDS although its prevalence appears to be low (less than 5%). In addition, the significance of LUC7L2 mutations is uncertain although in some reported cases it has been associated with disease progression. Further study is required.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 100% of Hairy cell leukemia, 40-70% of Langerhans cell histiocytosis, approximately 50% of Erdheim-Chester disease, approximately 5% of diffuse large B cell lymphoma and plasma cell neoplasms and less than 5% of chronic lymphocytic leukemia. While some reports have found that 10-20% of cases of acute leukemias (ALL or AML) may have BRAF mutations, other reports have described no BRAF in those diseases or in myeloid diseases such as MDS or CML. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain clinical settings.
EZH2 encodes the histone methyltransferase subunit of the polycomb repressive complex 2 (PRC2) that leads to H3K27me3 and promotes transcriptional repression. EZH2 loss of function mutations (nonsense, frameshift mutations, occasionally occurring as homozygous mutations) may occur throughout the gene and have been reported in less than 10% of patients with acute myeloid leukemia, myelodysplasia, atypical chronic myelogenous leukemia, primary myelofibrosis and up to 12% of patients with chronic myelomonocytic leukemia. EZH2 loss of function mutations may be more frequent (15%) among cases of T cell acute lymphoblastic leukemia. EZH2 mutations have been independently associated with adverse prognosis in MDS and MDS/MPN. Therapeutic targeting of EZH2 is currently under study for some types of lymphoma and solid tumors.
RAD21 belongs to the cohesin complex family of genes that encode protein subunits of the cohesion complex, which regulates chromosomal segregation. is a member of the cohesin complex that regulates chromosome segregation during meiosis and mitosis. Loss of function mutations of RAD21 have been described throughout the gene in approximately 1% of cases of myelodysplasia, 1-5% of acute myeloid leukemia (AML), 1% of chronic myeloid leukemia and tend to be mutually exclusive of other mutations in the other components of the cohesin complex (ie, STAG1, SMC3, STAG2, SMC1A). In AML, mutations in the cohesin complex genes tend to be associated with mutations in NPM1. Cohesin complex mutations do not have clear prognostic impact in AML. Cohesin complex mutations are associated with an unfavorable prognosis in myelodysplastic syndrome, and are more frequently found in patients with high IPSS scores and secondary acute myeloid leukemia.
JAK2 is a non-receptor tyrosine kinase that mediates signaling via the JAK-STAT pathway. The somatic, activating mutation V617F in the pseudokinase domain of JAK2 has been reported in over 90% of patients with polycythemia vera, 40-70% of essential thrombocythemia, 40-60% of primary myelofibrosis and 50% of MDS/MPN with Ring Sideroblasts and Thrombocytosis. JAK2 mutations have also been reported in CHIP. The small percentage of cases of polycythemia vera that do not carry the JAK2 V617F mutation have somatic, activating mutations in JAK2 exon 12 which typically affect the region encompassing codons 536-547 and are in-frame deletions/insertions, duplications of 8-12 amino acids or missense mutations. Mutations in JAK2 are typically mutually exclusive with mutations in the thrombopoietin receptor (MPL) and calreticulin (CALR), but JAK2 mutations may co-exist with mutations in other genes (ie, IDH1, SF3B1, TET2, ASXL1, etc). Ruxolitinib is a JAK2 inhibitor that has been approved for use in patients with intermediate- and high-risk primary myelofibrosis and is under study in other JAK2+ MPNs. Other JAK2 inhibitors (eg, Pacritinib) are also in various stages of study.
PAX5 is an important transcription factor in B cell development. Somatic deletions, rearrangements and mutations of PAX5 are seen in approximately 30% of B-ALL. Mutations most commonly include missense and frameshift mutations throughout the gene which typically lead to decreased transcriptional activation by PAX5. A frequent site of mutation is Pro80. Interestingly, a germline variant in PAX5 has been recently described (p.Gly183Ser) that is linked to family history of B-ALL and development of leukemia when associated with 9p deletion(loss of heterozygosity) and retention of the mutant allele in tumor cells; mutations at this codon have also been reported in tumors as a somatic alteration.
ABL1 kinase domain mutations in Philadelphia chromosome positive acute lymphoblastic leukemia and chronic myelogenous leukemia are associated with resistance to some types of tryosine kinase inhibitor therapy. The various mutations span several hundred amino acids (M237 thru E507) and vary in their response to later generation tyrosine kinase inhibitors.
NOTCH1 encodes a member of the NOTCH family of proteins, which is a group of transmembrane receptors involved in the Notch signaling pathway. Notch signaling regulates cell fate decisions during development, and plays a crucial role in T cell development. Activating mutations of NOTCH1 including missense mutations and inframe inserstions/deletions in the heterodimerization(HD) domains either alone or together with missense, nonsense or frameshift (in/del) mutations in the C terminal PEST domain have been described in approximately 50% of cases of T-ALL. The HD domain or PEST domain mutations may occur together in cis (on the same allele) in ALL. NOTCH1 mutations are very rare in AML. However, NOTCH1 mutations are present in about 27% patients with T-myeloid mixed-phenotypeacute leukemia. The potential utility of therapeutic targeting of activating NOTCH1 mutations in these diseases remains to be elucidated.
GATA 3 is a transcription factor important in T cell development and is known to be mutated in certain syndromes(hypoparathroidism, deafness, renal dysplasia). Missense, frameshift and insertion/deletion mutations in the zinc finger domain have been reported in 10-15% of early T cell precursor ALL and may be associated with biallelic mutations or concomitant deletion of the second allele.
PTEN is a lipid and protein phosphatase that negatively regulates the PI3K/AKT/mTOR pathway. PTEN has been reported to show nonsense and frameshift mutations in approximately 10% of adult T cell ALL patients. PTEN mutations may occur together with large deletions of PTEN which are not detected by this assay. PTEN abnormalities are thought to be more frequent in NOTCH1/FBXW7 unmutated T-ALL and appear to be mutually exclusive of NRAS/KRAS mutations in T-ALL. PTEN alterations are associated with reduced or absent protein expression and may be associated with a poor prognosis in adult T cell ALL, but not pediatric T-ALL, according to some studies. PTEN alterations appear to be infrequent among myeloid malignancies.
The cytosolic 5'-nucleotidase II gene (NT5C2), encodes a 5'-nucleotidase that is responsible for the inactivation of nucleoside-analog chemotherapy drugs. NT5C2 dephosphorylates and inactivates 6-thioinositol monophosphate and 6-thioguanosine monophosphate which mediate the cytotoxic effects of 6-mercaptopurine (6-MP) and 6-thioguanine (6-TG), two nucleoside analogs commonly used in the treatment of ALL. Activating mutations of NT5C2 have been reported in 19%of relapsed T cell ALLs and 3-10% of relapsed B-precursor ALLs. NT5C2 mutant proteins show increased nucleotidase activity and conferred resistance to chemotherapy with 6-mercaptopurine and 6-thioguanine, suggesting that relapse-specific mutations in NT5C2 may act as a mechanism of resistance to 6-MP and a genetic driver of relapse in ALL.
SMC3 is a member of the cohesin complex and has been found to be mutated in approximately 1% of acute myeloid leukemia and 1% myelodysplastic syndromes. The mutations of SMC3 described tend to be missense mutations that occur throughout the gene. Mutations of the various members of the cohesin complex appear to occur in a mutually exclusive manner. Cases of AML with mutations of the cohesin complex may be associated with mutations of NPM1. Currently there does not appear to be any clear prognosistic impact of cohesin complex gene mutations in AML. Cohesin complex mutations are associated with an unfavorable prognosis in myelodysplastic syndrome, and are more frequently found in patients with high IPSS scores and secondary acute myeloid leukemia.
WT1 encodes for a transcription factor containing an N-terminal transactivation domain and a C-terminal zinc-finger domain necessary for the development of the urogenital system. The precise roles of WT1 in normal and malignant hematopoiesis remain uncertain. New emerging supports a novel role of WT1 in the regulation of epigenetic programs through its interaction with TET proteins in the 5=hydroxymethylation of cytosines. WT1 mutations are found in 6% of acute myeloid leukemia overall, and about 8-13% in cytogenetically normal AML. Higher frequencies are present in biallelic CEBPA mutated acute myeloid leukemia (14%), followed by t(15;17)/PML-RARA (11.0%), and FLT3-ITD (8.5%,). WT1 mutations are associated with younger age in AML. WT1 mutations are typically putative loss of function mutations and most frequently occur in exon 7 or exon 9. About 75% of these mutations are frameshift, and the remaining are missense, nonsense, splice site or inframe indel mutations. In some cases two or more mutations in WT1 may occur. In addition, WT1 mutations may coexist with mutations in NPM1, FLT3, among others. WT1 is overexpressed in the majority of AML, giving rise to the concept that it may act as both a tumor suppressor and oncogene, depending on the context. Several studies showed that WT1 mutations are associated with a worse prognosis in cytogenetically normal acute myeloid leukemia, although one study including patients from three German-Austrian AML study protocols demonstrated no association with overall survival or relapse-free survival. Given its over-expression in AML, clinical trials employing peptide vaccination strategy against WT1 has been ongoing in AML patients.
SF1 is a member of the spliceosome machinery and missense mutations have been described in approximately 1% of myeloid neoplasms including myelodysplasia, acute myeloid leukemia and myeloproliferative neoplasms.
EED is a component of the polycomb repressor complex 2 (PRC2). Missense and frameshift mutations have been described in T cell acute lymphoblastic leukemia and may be enriched in the early T cell precursor subtype of that disease(found in appromimately 5% of such cases). In addition, mutations of EED have been described in, overall, less than 5% of myeloid neoplasms including cases of CMML, AML and MDS. EED mutations tend to be exclusive of mutations in EZH2, another component of PRC2. Deletions of EED have also been described which are not detected by this assay.
The ataxia telangiectasia mutated (ATM) gene is important in the cellular response to DNA double stranded breaks. ATM genetic abnormalities include deletions and mutations which may occur alone or together. ATM mutations have been reported to occur in approximately 35% of chronic lymphocytic leukemia; biallelic ATM inactivation (deletions and mutations) are associated with a poor outcome in some setttings compared to monoallelic ATM deletion or mutation in CLL. The ATM mutations occur throughout the gene and are putative loss of function variants (missense, nonsense and frameshift mutations). ATM mutations have also been reported in other types of lymphoma including mantle cell lymphoma (50%) and T cell prolymphocytic leukemia (46%).
CBL (casitas-B-lineage lymphoma) gene mutations have been identified in approximately 15% of chronic myelomonocytic leukemia, 15% of juvenile myelomonocytic leukemia, 15% of secondary AML(from MDS or MDS/MPN overlap syndrome) and rare or absent in polycythemia vera, essential thrombocythemia, primary myelofibrosis, chronic eosinophilic leukemia and MDS. Also, CBL mutations are found in only 1% of de novo acute leukemias and tend to be associated with core binding factor acute myeloid leukemia (AML) among AML cases. CBL is a Ras pathway gene and has been associated with hereditary myeloid disorders. CBL ubiquitinylates and degrades activated receptor and non-receptor tyrosine kinases via the E3-ligase activity of its RING domain. CBL also acts as an adaptor for downstream cell signal transduction, via its tyrosine kinase binding domain. Most variants of the CBL protein are missense substitutions in the zinc binding RING domain (amino acids 366-420) (exons 8-9) that abrogate CBL ubiquitin ligase activity but retain other functions. Pathogenic mutations are believed to be oncogenic by a variety of potential mechanisms including increased Ras pathway activation, aberrant phosphoSTAT5 and/or increased KIT expression in different cellular contexts. Occasionally, two CBL mutations may be present or CBL mutations may be associated with uniparental disomy. In addition, CBL mutations may occur together with mutations in other genes ( RUNX1, ASXL1, TET2 or EZH2 ). According to some studies, mutations of CBL may be associated with reduced overall survival in MDS.
ETV6 is a transcriptional repressor and is frequently involved in translocations with a variety of different partner genes in a range of hematologic malignancies. Mutations of ETV6 have been described in <5% of myelodysplastic syndromes and appear to be more frequent (ie, 10-24% of cases) in early T cell precursor type (immature) acute lymphoblastic leukemias. In addition, ETV6 mutations have been reported in association with hereditary myeloid disorders. These mutations occur throughout the gene and typically correspond to loss of function mutations (nonsense and frameshift mutations). ETV6 mutations may occasionally occur in a homozygous/hemizygous manner and tend to occur with mutations in NOTCH1 in lymphoblastic leukemia. In MDS, ETV6 mutations have been independently associated with an adverse prognosis. If clinical findings and family history are concerning for the presence of an inherited disorder, then genetic counseling may be helpful, if clinically indicated.
KRAS is a well known proto-oncogene that belongs to the small GTPase family and functions as a central mediator of downstream growth factor receptor signaling, with a critical role for cell proliferation and survival. Pathogenic mutations in KRAS typically occur in codons 12-13 of exon 2 and codon 61 of exon 3; however, other, non-canonical, pathogenic mutations in KRAS have also been reported in acute myeoid leukemia. KRAS mutations have been described in approximately 3-15% of acute myeloid leukemia, 8-20% of chronic myelomonocytic leukemia, 14% of juvenile myelomonocytic leukemia, 8% of blastic plasmacytoid dendritic cell neoplasm 4% of patients with myelodysplastic syndrome, 2% of primary myelofibrosis, 12% of B cell acute lymphoblastic leukemia (often associated with MLL rearrangement) and 1-2% of T cell acute lymphoblastic leukemia. Investigation into the targetability of this pathway in leukemia has been attempted in some disease models.
PRPF40B is a member of the RNA splicing machinery which has been reported to be rarely mutated (less than 5%) among cases of acute myeloid leukemia, myelodysplasia, chronic myelomonocytic leukemia and myeloproliferative neoplasms. Mutations in PRPF40B are typically missense mutations that may be located throughout the gene. PRPF40B mutations tend to be exclusive of other mutations in the spliceosome pathway.
SH2B3 encodes the lymphocyte adaptor protein (LNK) which attenuates JAK2 activation and negatively regulates the signaling of the thrombopoietin receptor (MPL) and the erythropoietin receptor. LNK has also shown to bind and regulate mutant signaling molecules found in myeloproliferative neoplasms (MPNs) like MPL-W515L and JAK2-V617F. Several acquired SH2B3 frameshift and missense mutations in the pleckstrin homology domain and NH2-terminal region have been reported in myeloproliferative neoplasms. Somatic mutations of SH2B3 are infrequent in MPN and reported in ~5 to 7% of MPN patients. These mutations can be found in all MPN subtypes and co-exist with other driver genes. In one study, SH2B3 mutations are associated with JAK2, CALR and MPL mutations in 50%, 18% and 13.6% of positive cases. All identified mutations were found throughout the gene, without evidence of a hot spot. SH2B3 mutations may be enriched in blast phase disease with a frequency up to 13% of such cases. Also, approximately 1% of T cell and B cell acute lymphoblastic leukemias have been shown to carry homozygous frameshift or nonsense mutations in SH2B3. Partial deletions of SH2B3 have also been reported in ALL. In addition, the T allele of a nonsynonymous single-nucleotide polymorphism (SNP), rs3184504 (p;W262R, c.784T>C), in exon 2 of the SH2B3 gene has been reported to be more prevalent among JAK2V617F-positive patients than control patients or JAK2 wild type patients. Loss of function mutations in SH2B3 have been shown to lead to increased JAK2/STAT3 signaling and cell proliferation.
PTPN11 encodes SHP2, a member of the non-receptor protein tyrosine phosphatase (PTP) family that regulates growth factor and cytokine signaling and plays a key role in the proliferation and survival of hematopoietic cells. PTPN11 mutation is directly associated with the pathogenesis of Noonan syndrome and childhood leukemias. Despite its direct function in protein dephosphorylation, SHP2 plays an overall positive role in transducing signals. Germline and somatic mutations that result in increased activity of PTPN11 have been described in Noonan's syndrome (approximately 50%), juvenile myelomonocytic leukemia (35-42%), pediatric and adult myelodysplasic syndromes (4-10%), B cell acute lymphoblastic leukemia (5-10%), as well as pediatric and adult acute myeloid leukemia (5-10%). These gain of function mutations most often occur as heterozygous missense mutations located in exon 3 (SH2 domain) or exon 13 (phosphatase domain) . Within cases of juvenile myelomonocytic leukemia, mutations of PTPN11 tend to be exclusive of mutations in RAS, CBL and NF-1. PTPN11 mutations in adult AML are associated with a normal karyotype and concurrent NPM1 mutation, but no alteration of the FLT3. In one study, myelodysplastic syndromes with PTPN11 mutations were shown to have a worse overall survival. Small molecule inhibitors of PTPN11 are currently being developed.
FLT3 is a receptor tyrosine kinase important in hematopoietic cell proliferation and differentiation. In-frame, FLT3 internal tandem duplications (ITD), which show a wide range of number of nucleotides duplicated and/or inserted (eg, 18-204 bp), affect exons 14 and 15 in the FLT3 juxtamembrane/tyrosine kinase domain and have been reported in 20-30% of patients with acute myeloid leukemia. FLT3 ITDs usually occur in cases of AML with a normal karyotype and but may also occur in cases with chromosome abnormalities including t(15;17) or other cytogenetic groups. Individuals with FLT3 mutations are more likely to have AML than MDS and FLT3 mutations in MDS are associated with a poor prognosis. Functional studies have shown that FLT3 ITDs are ligand-independent, gain-of-function mutations. In addition, activating mutations at codon D835 in exon 20 (A-loop of the tyrosine kinase domain, TKD) of FLT3 have been reported in approximately 7-10% of AML. The FLT3 D835 mutations are also ligand-independent, gain-of-function mutations. FLT3 ITD and D835 mutations tend to occur in a mutually exclusive manner; however, the FLT3 D835 mutation or other mutations in the A-loop(eg, D839, Y842) may occur as an acquired resistance mutation in the setting of patients with FLT3 ITD mutations being treated with targeted therapy. In addition, variants at codon N676 and in exon 17 F691, G697 have been associated with resistance to FLT3 targeted therapy. The presence of FLT3 ITD mutation in young patients with AML and normal cytogenetics is thought to be associated with a poor prognosis. On the other hand, the prognostic significance of the FLT3 D835 and TKD mutations appears less clear. More recently, therapeutic targeting of FLT3 in combination with other chemotherapy is available in certain settings for acute myeloid leukemia with FLT3 ITD or TKD mutations. Lastly, in T cell acute lymphoblastic leukemia, up to 20% of cases have been reported to show a FLT3 mutation (TKD or ITD) and are often associated with an ETP(early T cell precursor) phenotype. In addition, FLT3 mutations have also been reported in up to 15% of B-ALL cases ("Ph-like phenotype") and may also be associated with hyperdiploidy and MLL rearrangement. Targetting FLT3 in acute lymphoblastic leukemia therapy may also be possible in some settings.
PDS5B is a functional component of the cohesin complex which is very rarely mutated in myeloid neoplasms.
IDH2 is a mitochondrial enzyme involved in citrate metabolism. Mutations at Arg140 and Arg172 of IDH2 are typically heterozygous mutations and considered gain of function mutations that lead to increased levels of 2-hydroxyglutarate which is believed to alter epigenetic regulation (ie, DNA methylation) in AML. Mutations of IDH2 appear to be mutually exclusive of mutations in TET2, another gene involved in regulation of DNA methylation, and also exclusive of mutations in IDH1. Mutations of IDH2 have been shown to lead to increased DNA methylation in AML. IDH2 mutations have been reported in 10-20% of AML and are often associated with a normal karyotype. IDH2 mutations have been reported in less than 5% of cases of MDS and less than 10% of myeloproliferative neoplasms. The prognostic impact of IDH2 mutations in AML appears uncertain due to conflicting reports. In the setting of essential thrombocytosis, primary myelofibrosis and MDS, the presence of IDH2 mutations is associated with reduced survival. Therapeutic targeting with an FDA approved mutant IDH2 inhibitor (enasidenib (AG-221)) has been reported for patients with relapsed or refractory IDH2-mutated AML.
CREB binding protein (CREBBP) is considered to be an epigenetic regulator with diverse functions that include acetyltransferase activity, scaffolding function for transcription factor complexes and ubiquitin ligase activity. CREBBP mutations may occur as germline variants in Rubinstein Taybi syndrome and as somatic variants where they have been described in lymphoid malignancies. Missense, frameshift and nonsense mutations of CREBBP have been reported in 13-43% of B cell acute lymphoblastic leukemia and tend to occur in the HAT domain that is encoded by exons 18 through 29; more specifically, the missense mutations typically cluster in exons 25-27 of the HAT domain, however, mutations in other regions in the protein have been reported and may be important. CREBBP mutations have also been described in diffuse large B cell lymphoma and follicular lymphoma. Deletions/loss of heterozygosity of CREBBP has been described in ALL but are not detectable by this assay. Mutations of CREBBP appear to predominate in hyperdiploid B cell ALL, especially in such cases associated with disease relapse.
CTCF is a zinc finger protein involved in a variety of cell functions. Mutations of CTCF including missense, nonsense and frameshift mutations occur throughout the gene and have been reported in approximately 5% of acute megakaryoblastic leukemia, 2% of transient abnormal myelopoiesis, less than 5% of AML, less than 5% of MDS and less than 5% cases of ALL.
PRPF8 (Pre-MRNA Processing Factor 8) is a component of the RNA splicing machinery. Somatic PRPF8 mutations have been reported in less than 5% of cases of myelodysplastic syndrome/secondary AML and PRPF8 mutation status may be used, together with other clinical and molecular markers, in some prognostic models of MDS .
TP53 is a well known tumor suppressor gene that is mutated in wide variety of cancers. Loss of function mutations (missense, nonsense and frameshift mutations) of TP53 have been described in 10-20% of CLL cases and TP53 gene defects tend to be enriched among cases with unmutated IGH variable regions; in some series, TP53 mutations have been reported in approximately 15%-18% of IGHV unmutated CLL cases . TP53 mutations appears to be less common in other types of CLL (eg, less than 5% of IGHV3-21-expressing CLL carried a TP53 defect according to one study). Mutations of TP53 in CLL have been found together with del17p and mutations in other genes such as NOTCH1 and SF3B1. Mutations and deletions of TP53 appear to represent adverse prognostic markers in chronic lymphocytic leukemia.
IKZF3 is a member of the IKAROS family of transcription factors which are important in lymphoid development. Missense and frameshift mutations of IKZF3 have been reported in approximately 10% of chronic phase and matched blast phase of CML , approximately 10% of blastic plasmacytoid dendritic cell neoplasms and rare cases of acute lymphoblastic leukemia.
Signal transducer and activator of transcription 3 gene (STAT3) plays an important role in the JAK/STAT signaling pathway induced by cytokine and growth factor receptor activation. STAT3 mutations have been reported in approximately 40% of cases of T-cell large granular lymphocytic leukemia and one third of NK cell lymphoproliferative disorders; these mutations are typically missense mutations or inframe insertions mutations in exons 20 and 21 which encode the Src homology 2 (SH2) domain that mediates the dimerization and activation of STAT protein; these mutations are typically associated with increased transcriptional activity. In addition, the presence of STAT3-mutant T-LGL clones may be found in a subset of patients with aplastic anemia and/or myelodysplastic syndrome. Therapeutic targetting of STAT3 is currently under investigation in various settings.
CD79B is a component of the cell surface B cell receptor complex and is upstream of the NFkB signaling pathway. CD79B mutations at Tyr196 have been reported in approximately 20% of primary testicular diffuse large B cell lymphomas and approximately 10-15% of diffuse large B cell lymphomas overall. CD79B mutations are typically associated with increased cell surface expression of CD79B due to attenuation of the usual negative feedback by LYN kinase. CD79B mutations have been reported to coexist with MYD88 mutations and may be enriched in the activated B cell type of diffuse large B cell lymphoma. The potential for therapeutic targeting of this pathway is currently under investigation.
SRSF2 is a member of the serine/arginine-rich family of pre-mRNA splicing factors, which constitute part of the spliceosome. It interacts with other spliceosomal components bound to both the 5- and 3-splice sites during spliceosome assembly. SRSF2 mutations typically occur as missense mutations at Pro95. SRSF2 mutations have been reported in approximately 40% of cases of chronic myelomonocytic leukemia, but they may not have prognostic significance in that entity. Comutation of TET2 and SRSF2 was highly predictive of a myeloid neoplasm characterized by myelodysplasia and monocytosis, including but not limited to, chronic myelomonocytic leukemia. In addition, SRSF2 mutations have been reported in approximately 15-20% of cases of myelodysplastic syndrome. SRSF2 mutations have also been described in 5-20% of patients with acute myeloid leukemia and appear to be enriched among AML patients with reduced blast counts. SRSF2 has been found to be mutated in approximately 10% of cases of primary myelofibrosis where mutations may occur together with mutations in JAK2, MPL, TET2, CBL, ASXL1, EZH2, IDH1/2. SRSF2 mutations are also present in 8% of blastic plasmacytoid dendritic cell neoplasm and 3% of polythemia vera. SRSF2 mutations tend to be (although are not entirely) exclusive of mutations in other splicing factor components. SRSF2 mutations are associated with a poor prognosis in myelodysplastic syndrome (NCCN Guidelines for Myelodysplastic Syndromes), primary myelofibrosis, polycythemia vera, and KIT D816V-mutated advanced systemic mastocytosis. SRSF2 mutations are also reported to be highly specific for secondary acute myeloid leukemia, and may also be helpful in identifying a subset of elderly patients with de novo acute myeloid leukemia and therapy-related AML with worse clinical outcomes.
SETBP1 encodes a protein which is believed to inhibit PP2A phosphatase activity through SET stabilization. In addition, SETBP1 binds to gDNA in AT-rich promoter regions, causing activation of a network of development genes through recruitment of a HCF1/KMT2A/PHF8 epigenetic complex. Heterozygous, somatic, missense mutations are predominantly hot-spot mutations within the SKI homologous region in exon 4, which result in the functional loss of the degron motif responsible for the short half-life of the protein. Therefore, these mutations result in an increased half-life and accumulation of the mutated SETBP1, and thus increased inhibition of the oncosupressor PP2A through the SETBP1-SET-PP2A axis. In addition, mutations in SETBP1 potentially deregulate gene transcription mediated by SETBP1. SETBP1 mutations have been described in approximately 25% of atypical chronic myelogenous leukemia, 30% of juvenile myelomonocytic leukemia, 17% of secondary acute myeloid leukemia, 13% of myeloproliferative/myelodysplastic syndrome with ring sideroblasts and thrombocytosis, and 5-15% of chronic myelomonocytic leukemia. SETPB1 mutations appear to be rare (< 5%) or absent among cases of primary acute myeloid leukemia, acute lymphoblastic leukemia, myelodysplastic syndromes, myeloproliferative neoplasms and chronic lymphocytic leukemia. SETBP1 mutations may be seen together with mutations in other genes such as ASXL1. Mutated SETBP1 provides supportive evidence for the diagnosis of atypical chronic myeloid leukemia, BCR-ABL1-negative in the 2016 revision of the WHO classification.SETBP1 mutations are associated with disease progression in myelodysplastic syndrome (NCCN Guidelines for Myelodysplastic Syndromes), and unfavorable prognosis in chronic myelomonocytic leukemia, juvenile myelomonocytic leukemia, atypical chronic myeloid leukemia, and MDS/MPN with ring sideroblasts associated and thrombocytosis.
JAK3 is a member of the Janus family of tyrosine kinases, which are involved in cytokine receptor-mediated signaling through the JAK/STAT pathway. JAK3 is believed to be essential for the development of lymphoid cells, especially mature T-cells and NK cells. Missense mutations of JAK3 have been described in approximately 34% of T cell prolymphocytic leukemias, 20% of natural killer cell lymphoma, 10% of T cell acute lymphoblastic leukemia including early T cell precursor T cell ALL and occasional cases of Down syndrome associated -myeloid leukemia, -transient leukemia and -acute megakaryoblastic leukemia. In addition, subclonal, secondary mutations of JAK3 have been reported in approximately 10% of juvenile myelomonocytic leukemia and may occur together with mutations the RAS pathway genes. Mutations of JAK3 are typically activating (gain of function) mutations and are potential therapeutic targets in some settings.
MEF2B is a calcium-regulated transcription factor that recruits histone-modifying enzymes. Missense and truncating MEF2B mutations have been reported in the MADS box and MEF2B domains in up to 5% of cases of mantle cell lymphoma, and up to 20% of diffuse large B cell lymphoma and follicular lymphoma.
Mutations of the transcription factor CEBPA (CCAAT/enhancer binding protein alpha) have been reported in approximately 15% of patients with acute myeloid leukemia (AML) with a normal karyotype. CEBPA plays a role in the differentiation of granulocytes. Two types of mutations have been reported: N-terminal changes which result in a truncated dominant negative isoform lacking one of the N terminal domain transactivation domains and C-terminal mutations which are in-frame insertions or deletions affecting the leucine zipper and preventing dimerization and DNA binding. Patients may carry both N- and C-terminal mutations affecting different alleles. Isolated, biallelic ("double") mutations (not single mutation) of CEBPA appear to be associated with a favorable-risk group of normal karyotype AML. CEBPA mutations have also been reported in association with hereditary myeloid disorders; 5-10% of CEBPA double mutant AML cases may harbor germline mutations. Recommend correlation with clinical findings including family history and genetic counseling, if there is clinical suspicion of an inherited disorder.
CNOT3 is part of the CCR4-NOT complex that regulates gene expression and may act as a tumor suppressor. CNOT3 is mutated in approximately 8% of adult T cell acute lymphoblastic leukemia cases.
U2AF2 (U2AF65) is a member of the RNA splicing machinery and has been be reported to show missense mutations in less than 1% of cases of myelodysplastic syndromes and approximately 1% of cases of chronic myelomonocytic leukemia.
ASXL1 regulates epigenetic functions including histone and chromatin modifications. ASXL1 mutations have been reported in 40-50% of chronic myelomonocytic leukemia(CMML), 20% of myelodsyplastic syndromes, 20-35% of primary myelofibrosis, 15% of systemic mastocytosis, 30% of patients with secondary acute myeloid leukemia and 5-10% of primary acute myeloid leukemia. ASXL1 mutations have also been described in CHIP and CCUS. In CMML, missense mutations of ASXL1 appear to be less common (less than 10% of cases). Nonsense and frameshift mutations (but apparently not missense mutations) of ASXL1 have been reported to carry an adverse prognostic impact in cases of chronic myelomonocytic leukemia. In addition, ASXL1 mutations have been associated with adverse outcome in myelodysplasia, primary myelofibrosis and systemic mastocytosis. Among cases of AML, ASXL1 mutations appear to be associated with adverse prognosis in some subtypes of AML according to some, but not all, studies. ASXL1 mutations may coexist with mutations of splicing factor components, TET2 and RUNX1; for example, co-existence of U2AF1 and ASXL1 mutations have been described in CMML and primary myelofibrosis; While in AML, ASXL1 mutations have been reported to be exclusive of NPM1 mutations according to some studies.
GNAS (Guanine Nucleotide Binding Protein, Alpha, Stimulating Activity Polypeptide, G-S-alpha) is a component of the heterotrimeric G protein complex that has been shown to be mutated in less than 1% of myelodysplastic syndrome. Mutations of Arg201 of GNAS are typically activating mutations which have been described in various types of solid tumors and McCune Albright syndrome.
RUNX1(AML1, CBFA2) encodes the alpha subunit of core binding factor and is a transcription factor important in normal hematopoietic development. RUNX1 mutations have been reported in approximately 10% of myelodysplastic cases, 5-15% of acute myeloid leukemia, 8-37% of chronic myelomonocytic leukemia, 10% of T cell acute lymphoblastic leukemia, 3% of systemic mastocytosis, 2% of essential thrombocythemia and 2% of polycythemia vera. The mutations include frameshift, missense, nonsense, and splice site mutations. Typically, the Runt domain and the region just downstream of the Runt domain are affected and the mutations tend to be monoallelic. AML with RUNX1 mutation which does not fulfill the diagnostic criteria for other specific AML subtypes in the categories of AML with recurrent genetic abnormalities, therapy-related myeloid neoplasms, or AML with myelodysplasia-related changes is now classified the provisional entity of AML with mutated RUNX1. RUNX1 mutations may be associated with Trisomy 8 or MLL-PTD in AML according to some studies. They tend not to occur in AML cases with favorable cytogenetic findings and appear to be exclusive of NPM1 or CEBPA mutations in AML. Myeloid neoplasms, predominantly MDS/AML, developing in patients, usually at a young age, with a familial platelet disorder and germline monoallelic RUNX1 mutations are categorized as myeloid neoplasms with germline RUNX1 mutation. Of note, RUNX1 may also be involved in large intragenic deletions and translocations (e.g., t(8;21)(RUNX1-ETO), t(3;21)(RUNX1-EVI1), t(12;21)(TEL-RUNX1) which are not detected by this assay. Mutated RUNX1 is a poor-risk prognostic marker in AML unless it co-occurs with favorable-risk AML subtypes (NCCN Guidelines for AML). RUNX1 nonsense or frameshift mutations are associated with an unfavorable prognosis in myelodysplastic syndrome, independent of IPSS, IPSS-R, age, and other gene mutations (NCCN Guidelines for Myelodysplastic Syndromes). RUNX1 mutations are independently associated with unfavorable outcomes and shorter survival after hematopoietic stem cell transplantation in patients with myelodysplastic syndrome and myelodysplastic syndrome/acute myeloid leukemia. RUNX1 mutations are also associated with an unfavorable prognosis chronic myelomonocytic leukemia and systemic mastocytosis.
U2AF1 encodes for the small subunit of the U2 auxiliary factor, which is a non-small nuclear ribonucleoprotein (non-snRNP) required for the binding of U2 snRNP to the pre-mRNA branch site and plays critical role in RNA splicing. U2AF1 is one of several spliceosome complex genes frequently mutated in a variety of hematologic malignancies. Two hotspot mutations (S34 in exon 2 and Q157 in exon 6) occur within the two zinc-finger domains of the U2AF1 protein. These mutations have been reported in approximately 4- 9% of chronic myelomonocytic leukemia, 8-11% of cases of myelodysplastic syndrome (typically without ring sideroblasts), 16% of primary myelofibrosis, 12% of blastic plasmacytoid dendritic cell neoplasm, 4% of acute myeloid leukemia and 1% of essential thrombocythemia. U2AF1 mutations are associated with an unfavorable prognosis in myelodysplastic syndrome (NCCN Guidelines for Myelodysplastic Syndromes) and essential thrombocythemia, and decreased response to lenalidomide in myeloid neoplasms with and without del(5q). U2AF1 mutations are also reported to be highly specific for secondary acute myeloid leukemia, and may also be helpful in identifying a subset of therapy-related AML or elderly de novo AML with worse clinical outcomes. U2AF1 mutations have been associated with altered splicing patterns in vitro and in vivo, and may play a significant role in the pathogenesis of myeloid malignancies due to selective mis-splicing of tumor-associated genes.
SF3A1 is a component of the RNA splicing machinery. Missense mutations of SF3A1 are rare in myelodsyplasia, chronic myelomonocytic leukemia and acute myeloid leukemia (less than 2% of cases).
EP300 is a histone acetyltransferase and transcriptional coactivator. Somatic mutations of EP300 have been described in cases of T cell acute lymphoblastic leukemia and other lymphoid malignancies including diffuse large B cell lymphoma and follicular lymphoma. Occasional splice site mutations have also been described which are not detected by this assay. EP300 mutations have also been described in the Rubinstein-Taybi developmental syndrome.
Cytokine receptor-like factor 2 (CRLF2) is a type I cytokine receptor subunit that dimerizes with IL7R to form the receptor for thymic stromal lymphopoietin (TSLP). Heterozygous, somatic, gain-of-function mutations introducing cysteines in the transmembrane domain have been described in up to 20% of B cell acute lymphoblastic leukemias (ALL). These mutations cause ligand independent dimerization via disulfide bonds. The disulfide bond is critical for the activation since elimination of the cysteines abrogated the cytokine independent growth. In addition, more recently, another activating, non-cysteine mutation in the heterodimerization domain of CRLF2 has been reported.
ZRSR2 endoes a component of the RNA splicing machinery which associates with the U2 auxillary factor and is involved in the recognition of the 3'-splice site during the stages of spliceosome assembly. Mutations in ZRSR2 have been reported in approximately 3-11% of myelodysplasia, 4-8% of chronic myelomonocytic leukemia, 8% of blastic plasmacytoid dendritic cell neoplasm and less than 5% of acute myeloid leukemia and myeloproliferative neoplasms. Unlike other spliceosomal genes, ZRSR2 mutations do not occur in select "hot spots". Nearly all reported mutations are nonsense or frameshift mutations, compatible with loss-of-function mutations and suggesting a tumor suppressor role of ZRSR2. ZRSR2 mutations tend to be exclusive of mutations in most other components of the RNA splicing machinery. Aberrant splicing of U12-type introns has been shown to be a hallmark feature of MDS with ZRSR2 mutations. ZRSR2 mutations are associated with an unfavorable prognosis in myelodysplastic syndrome (NCCN Guidelines for Myelodysplastic Syndromes). ZRSR2 mutations are also reported to be highly specific for secondary acute myeloid leukemia, and may also be helpful in identifying a subset of therapy-related AML and elderly de novo AML with worse clinical outcomes.
BCOR is a ubiquitously expressed nuclear protein that is a transcriptional corepressor important in several cellular processes. Somatic, nonsense and frameshift mutations throughout BCOR have been reported in approximately 7% of chronic myelomonocytic leukemia, 4% of patients with myelodysplastic syndrome(MDS), 4% of primary acute myeloid leukemia and appear to be associated with RUNX1 and DNMT3A mutations . Also, BCOR mutations may be enriched among cases of AML lacking NPM1, CEBPA, FLT3-ITD, IDH1 and MLL-PTD alterations. BCOR mutations tend to be subclonal in MDS, clonal in primary AML and are believed to have significance as loss of function mutations in a tumor suppressor gene that affect the functional allele in male and female patients. The presence of BCOR mutation in patients with MDS and AML has been associated with poorer overall survival according to some studies.
The GATA1 transcription factor is important in the development of erythroid and megakaryocytic lineages. Amino-terminal, small insertion/deletion(frameshift), nonsense and missense mutations of GATA1 have been described in almost all patients with transient abnormal myelopoiesis(TAM) and acute megakaryoblastic leukemia associated with Down syndrome (Trisomy 21)(DS-AMKL). Studies suggest that the cases of TAM which progress to DS-AMKL are associated with the acquisition of additional driver mutations in other genes including the cohesin complex genes as well as CTCF and EZH2. The amino-terminal GATA1 mutations lead to a lack of the N-terminal amino acids and translation from an alternate start codon (methionine at position 84 in exon 3). GATA1 mutations appear to be rare in acute megakaryoblastic leukemia not associated with Down syndrome. GATA1 mutations have also been reported in the context of hereditary myeloid disorders. If clinical findings and family history are concerning for an inherited disorder, then genetic counseling may be helpful, if clinically indicated.
SMC1A belongs to the cohesin complex family of genes that encode protein subunits of the cohesion complex, which regulates chromosomal segregation. SMC1A has been reported to show somatic, missense mutations throughout the gene in less than 5% of cases of acute myeloid leukemia and less than 5% of chronic myeloid leukemia. Mutations of SMC1A are mostly mutually exclusive of mutations in other components of the cohesin complex. Mutations of SMC1A may be enriched in male patients since the gene is located on the X chromosome. Cohesin complex mutations are associated with an unfavorable prognosis in myelodysplastic syndrome, and are more frequently found in patients with high IPSS scores and secondary acute myeloid leukemia.
STAG2 belongs to the cohesin complex family of genes that encode protein subunits of the cohesion complex, which regulates chromosomal segregation. STAG2 has been reported to show somatic, nonsense, frameshift and occasional missense mutations throughout the gene in 6% of cases of myelodysplasia, 10% of chronic myelomonocytic leukemia, 6% of cases of acute myeloid leukemia, and less than 5% of chronic myeloid leukemia and myeloproliferative neoplasms. Mutations of STAG2 are mostly mutually exclusive of mutations in other components of the cohesin complex. STAG2 mutation is associated with a poor prognosis in myelodysplastic syndrome (NCCN Guidelines for Myelodysplastic syndromes). STAG2 mutations are also reported to be highly specific for secondary acute myeloid leukemia, and may also be helpful in identifying a subset of elderly patients with de novo acute myeloid leukemia or therapy-related AML with worse clinical outcomes.
BCORL1 is a transcriptional corepressor and putative tumor suppressor gene. Somatic, nonsense and frameshift mutations have been reported throughout BCORL1 in 6% of acute myeloid leukemia, 10% of patients with acute myeloid with myelodysplasia related changes, less than 1% of myelodysplasia and less than 2% of chronic myelomonocytic leukemia. BCORL1 is located on the X-chromosome.
PHF6 encodes a member of the plant homeodomain (PHD)-like finger (PHF) family with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation. It is localized to the nucleolus and may play a role in recognizing methylation status of histone lysines. Somatic, nonsense, frameshift and occasional missense mutations throughout PHF6 have been reported in up to 38% of cases of T cell acute lymphoblastic leukemia. In T-ALL, PHF6 mutations often co-exist with NOTCH1 mutations. PHF6 mutations have also been reported in approximately 3% of cases of acute myeloid leukemia, less than 5% of chronic myeloid leukemia in blast phase, and 3% of myelodysplastic syndrome. In acute myeloid leukemia, PHF6 mutations have been associated with male preponderance and reduced overall survival in patients with normal karyotype or intermediate-rish cytogenteics abnormalities. Mutated PHF6 is more frequent in MDS cases with excess blasts, but there appears to be no association with survival (NCCN Guidelines for Myelodysplastic Syndromes). PHF6 mutation status does not appear to affect outcome in T-ALL according to some studies.
RPL10 is a ribosomal protein of the 60S ribosomal subunit and shows missense mutations in approximately 5-8% of pediatric patients with T-cell acute lymphoblastic leukemia. The most common mutation is at p.Arg98. Functional studies suggest that the p.Arg98Ser mutation of RPL10 is associated with a ribosomal biogenesis defect. RPL10 is located on the X chromosome and RPL10 mutations may be enriched in male patients.
BRCC3 is a component of the DNA repair pathway. Nonsense and missense mutations have been reported in less than 5% of myelodysplasia.
Calreticulin(CALR) is an endoplasmic reticulum chaperone protein. Somatic insertions and deletions in exon 9 of calreticulin that cause a +1bp frameshift and a novel carboxy-terminal peptide in mutant calreticulin have been reported in 70% of JAK2/MPL-negative essential thrombocythemia (ET)and 56-88% of JAK2/MPL-negative primary myelofibrosis(PMF). In addition, CALR mutations have been reported in approximately 10% of patients with myelodysplasia, including JAK2/MPL-negative refractory anemia with ring sideroblasts (RARS-T) where it may co-occur with mutations in SF3B1. In ET, PMF, and RARS-T, calreticulin mutations appear to be mutually exclusive of mutations in JAK2 or MPL. The CALR mutations lead to loss of the endoplasmic reticulum retention motif (KDEL) sequence in the carboxy-terminal portion of mutant CALR. Calreticulin mutations appear to be absent in polycythemia vera, acute myeloid leukemia, chronic myeloid leukemia, systemic mastocytosis, lymphoid malignancies and are rare in atypical chronic myeloid leukemia and chronic myelomonocytic leukemia. The most common 52bp deletion mutation (Type 1) in CALR has been shown to lead to cytokine-independent growth and activation of STAT5. Type 2 (5 bp insertion) mutations have also been described. This represents a potentially targettable pathway alteration. Patients with some types of mutant CALR may show improved survival and lower risk of thrombosis compared to patients with mutant JAK2, according to some, but not all studies.
MAP2K1(MEK1) is a kinase which is downstream of BRAF and upstream of ERK-1/-2 in the MAPK pathway. MAP2K1 missense mutations and small in frame deletions have been reported in approximately 50% of hairy cell leukemia-variant (HCL-variant) cases, regardless of IGHV4-34–status, and greater than 50% of cases of IGHV4-34–positive classic hairy cell leukemia (classic HCL). These mutations are predicted to increase the basal enzymatic activity. MAP2K1 mutations appear to be mutually exclusive of the BRAF p.Val600Glu mutation, which appears to be largely specific to IGHV4-34–negative, classic HCL. Nevertheless, MAP2K1 mutations have been described as a mechanism of resistance to targetted therapy with BRAF inhibitors. The MAPK pathway alterations are potentially targetable.
Paroxysmal nocturnal hemoglobinuria (PNH) is a rare acquired hemolytic disorder that shows intravascular hemolysis and hemoglobinuria. Other clinical findings include thrombocytopenia and/or leukocytopenia and recurrent venous thrombosis. PNH results from the expansion of an abnormal clone of hematopoietic stem cells harboring somatic mutation in phosphotidylinositol glycan complementation class A (PIGA) gene, which appears to have a survival advantage. The PIGA gene maps to Xp22.1; therefore only one allele of PIGA is transcribed in both sexes because of X inactivation. Pathogenic mutation results in a deficiency in the surface expression of all GPI-anchored proteins (GPI-AP) because of defective synthesis of glycosylphosphatidylinositol (GPI). In all reported cases of acquired PNH, the mutation is detected only in the PIGA gene. PIGA germline mutations have been described in Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome 2 . Pathogenic mutations in PIGA tend to be nonsense, frameshift and occasionally splice site and missense mutations occurring throughout the gene. Detection of PNH clones by flow cytometry is done by studying the expression of GPI-AP on RBC and PB leukocytes using monoclonal antibodies specific for these proteins or by studying the GPI anchor itself, using FLAER. Correlation with other clinical and lab findings as well as family history is recommended. Genetic counseling may be helpful, if clinically indicated.
Despite pre-clinical data and case reports of response to EGFR inhibitors, the EGFR inhibitor gefitinib does not appear to be effective in the treatment of advanced AML .
Guanine nucleotide binding protein (G protein), beta polypeptide 1(GNB1) encodes a beta subunit of heterotrimeric G-proteins. Recurrent missense mutations at the Lys57 codon of GNB1 (eg, p.K57E, p.K57N, p.K57T) in the WD40 repeat motif have been reported in less than 5 % of myelodysplasia/secondary acute myeloid leukemia and de novo AML. The lysine at codon 57 of GNB1 has been reported to interact with the G-protein subunit alpha(GNAS), which itself has also been shown to be recurrently mutated in myelodysplasia. According to some studies, Lys57Ala mutations lead to altered downstream signaling in some G-protein coupled receptor signaling pathways. Overall, these findings suggests that mutations at Lys57 of GNB1 are pathogenic. In addition, frameshift mutation at codon 53 of GNB1 has also been described in myelodysplasia.
AKT1 mutations have been reported in a variety of tumor types such as endometrial, lung, breast, colorectal, ovarian, and prostate cancers. The mutations are mutually exclusive from PIK3CA mutations. Increased expression and activation of AKT1 observed in many cancers is caused by a variety of different mechanisms including genomic alterations of AKT1, PIK3CA, PTEN, RAS family members, or growth factor receptors. Gain-of-function alterations of AKT1 can lead to neoplastic transformation in model systems, and is a potential target for therapeutic strategies. The E17K variant is by far the most frequent AKT1 mutation reported, implicating it as an important tumor promoting event.
Somatic APC mutations are common events in colorectal adenocarcinomas, reported in up to 76% of the cases. Loss of normal APC function is known to be an early event in both familial and sporadic colon cancer pathogenesis, occurring at the pre-adenoma stage. APC mutations do not appear to significantly affect the prognosis of colorectal cancer patients. While there are a number of small molecule inhibitors in development that target the Wnt pathway, there is currently no matched targeted therapy available for colorectal cancer patients harboring an APC mutation.
Somatic APC mutations are common events in colorectal adenocarcinomas, reported in up to 76% of the cases. Loss of normal APC function is known to be an early event in both familial and sporadic colon cancer pathogenesis, occurring at the pre-adenoma stage. APC mutations do not significantly affect the prognosis of colorectal cancer patients. While there are a number of small molecule inhibitors in development that target the Wnt pathway, there is currently no matched targeted therapy available for colorectal cancer patients harboring an APC mutation.
Familial adenomatous polyposis (FAP) is a disease with autosomal-dominant inheritance that predisposes to carcinoma of the colorectum, stomach, duodenum, and thyroid. There is increasing evidence that germline variants in APC (E1317Q) predispose to the development of multiple colorectal adenomas and carcinoma.
Germline APC mutations are characteristically associated with Familial Adenomatous Polyposis (FAP) that predisposes to carcinomas of the colo-rectum, stomach, duodenum, and thyroid. Recently somatic mutations in exon 15 of APC gene have been described in certain sporadic papillary thyroid carcinomas. The prognostic impact of these mutations remains unknown in such settings.
APC mutations have been reported in lung squamous cell carcinoma and small-cell lung carcinoma, but rarely in lung adenocarcinoma. However, variants in the APC gene have not been well characterized in lung adenocarcinoma and their clinical significance is unclear. According to ClinVar, this particular variant is a likely benign germline variant (https://preview.ncbi.nlm.nih.gov/clinvar/variation/829/).
ATM alterations have been reported as germline variants which predispose to inherited cancer syndromes and as somatic (acquired) variants in tumors. ATM is part of many signalling networks, including cell metabolism and growth, oxidative stress, and chromatin remodelling, all of which can affect cancer progression. Although ATM is considered to be a tumour suppressor, ATM signaling may be advantageous to cancer cells in some settings, particularly in resistance to radio- and chemotherapeutic treatment. For this reason, the use of ATM inhibitors in cancer therapy is under exploration.
ATM alterations have been reported as germline variants which predispose to inherited cancer syndromes and as somatic (acquired) variants in tumors. ATM is part of many signalling networks, including cell metabolism and growth, oxidative stress, and chromatin remodelling, all of which can affect cancer progression. Although ATM is rightly considered to be a tumour suppressor, ATM signalling can also be advantageous to cancer cells, particularly in resistance to radio- and chemotherapeutic treatment. For this reason, ATM inhibitors have been developed for use in cancer therapy.
ATM alterations have been reported as germline variants which predispose to inherited cancer syndromes and as somatic (acquired) variants in tumors, including breast cancer. ATM is part of many signalling networks, including cell metabolism and growth, oxidative stress, and chromatin remodelling, all of which can affect cancer progression. Although ATM is rightly considered to be a tumour suppressor, ATM signalling can also be advantageous to cancer cells, particularly in resistance to radio- and chemotherapeutic treatment. For this reason, ATM inhibitors have been developed for use in cancer therapy.
Eighty percent of all thyroid cancers are papillary thyroid carcinomas (PTCs). BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and V600E is an activating mutation of BRAF. The BRAF V600E mutation has been reported in 45% of patients with papillary thyroid carcinoma. The BRAF V600E-like PTC's (BVL) and the RAS-like PTC (RL-PTC) are fundamentally different in their genomic, epigenomic, and proteomic profiles. Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC , other well-differentiated thyroid neoplasms or nodular goiters. The possible prognostic impact of BRAF V600E mutations in papillary carcinoma of the thyroid continues to be studied. FDA approved dabrafenib and trametinib administered together for the treatment of BRAF V600E mutation-positive anaplastic thyroid cancer.
Presence of a BRAF c.1799T>A, p.Val600Glu (V600E) mutation in a microsatellite unstable colorectal carcinoma indicates that the tumor is probably sporadic and not associated with Lynch syndrome (HNPCC). However, if a BRAF mutation is not detected, the tumor may either be sporadic or Lynch syndrome associated. Detection of BRAF mutations may also be useful in determining patient eligibility for anti-EGFR treatment. Approximately 8--15% of colorectal cancer (CRC) tumors harbor BRAF mutations. The presence of BRAF mutation is significantly associated with right-sided colon cancers and is associated with decreased overall survival. Some studies have reported that patients with metastatic CRC (mCRC) that harbor BRAF mutations do not respond to anti-EGFR antibody agents cetuximab or panitumumab in the chemotherapy-refractory setting. BRAF V600-mutated CRCs may not be sensitive to V600E targeted TKIs. Drug: Vemurafenib + Panitumumab, Encorafenib + Binimetinib + Cetuximab, Radiation + Trametinib + Fluorouracil
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are present in approximately 50% to 60% of cutaneous melanomas and are also present at lower frequencies in other melanoma subtypes. The hotspot for mutations in BRAF is at codon Val600 and the most common one is p.Val600Glu (V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for melanoma therapy in certain settings. Drug: Vemurafenib Dabrafenib Dabrafenib + Trametinib Vemurafenib + Cobimetinib Trametinib
Somatic mutations in BRAF have been found in 1-4% of all NSCLC most of which are adenocarcinomas and may be a potential therapeutic target in some settings. Drug: Vemurafenib, Dabrafenib, Dabrafenib + Trametinib
Somatic mutations in BRAF have been found in 1-4% of all NSCLC most of which are adenocarcinomas. The G469A mutation results in an amino acid substitution at position 469 in BRAF, occurs within the highly conserved motif of the kinase domain. Most mutant BRAF proteins, such as G469A, have increased kinase activity and are transforming in vitro. In preclinical studies, lung cancer cell lines harboring the BRAF G469A mutation were not sensitive to dasatinib
Somatic mutations in BRAF have been found in up to 10% of all NSCLC, more common in adenocarcinomas. The G464V mutation results in an amino acid substitution within the highly conserved motif of the kinase domain. This specific mutation is a low frequency cancer-associated variant classified as an intermediate activity mutant that moderately increases ERK activation and can transform cells. The predictive significance of this mutation needs further study. Clinical correlation is recommended.
Somatic mutations in BRAF have been found in 1-4% of all NSCLC most of which are adenocarcinomas. The K601E mutation results in an amino acid substitution at position 601 in BRAF, occurs within the highly conserved motif of the kinase domain. Most mutant BRAF proteins, such as K601E, have increased kinase activity and are transforming in vitro. Preclinical studies suggest that downstream signaling induced by the K601E mutant may be blocked by the BRAF inhibitor, vemurafenib.
The D594E mutation in BRAF is believed to result in inactivation of BRAF and, therefore, BRAF inhibitors are not likely to be effective.
BRAF alterations have been described in a wide spectrum of brain tumors, including in gliomas and glioneuronal tumors. BRAFV600E mutations have been found in approximately 10--15% of pilocytic astrocytoma and in approximately 5--10% of pediatric diffusely infiltrating gliomas, including diffuse astrocytomas (WHO grade II), anaplastic astrocytomas (WHO grade III) and glioblastomas (WHO grade IV), but in less than 2% of comparable adult gliomas. This mutation is potentially targetable.
BRAF mutants, with a 3bp insertion between codons 599 and 600, display increased in vitro kinase activity activation potential comparable to those of BRAF V600E mutants.
Somatic mutations in CTNNB1 (Beta-catenin) have been found in ~2-3% of malignant melanomas. Preclinical models have demonstrated that concurrent mutations in Beta-catenin and NRAS are synergistic in promoting melanoma formation.
CTNNB1 encodes the protein b-catenin, a transcriptional activator involved in the WNT signaling pathway. Somatic gain-of-function mutations in CTNNB1 result in aberrant accumulation of the b-catenin protein and are prevalent in a wide range of solid tumors, including endometrial carcinoma, ovarian carcinoma, hepatocellular carcinoma, and colorectal carcinoma, among others. Genetic alterations in CTNNB1 have been identified in 4% of non-small cell lung cancers. The CTNNB1 S45P mutation is likely oncogenic, but no real progress has been made in targeting oncogenic mutant forms of CTNNB1 in lung cancer. However, CTNNB1 mutation-positive cancers are presumed to be resistant to pharmacologic inhibition of upstream components of the WNT pathway, instead requiring direct inhibition of b-catenin function. In one study pharmacological inhibition of b-catenin suppressed EGFR-L858R/T790M mutated lung tumor and genetic deletion of the b-catenin gene dramatically reduced lung tumor formation in transgenic mice, suggesting that b-catenin plays an essential role in lung tumorigenesis and that targeting the b-catenin pathway may provide novel strategies to prevent lung cancer development or overcome resistance to EGFR TKIs. These results should be interpreted in the clinical context.
CTNNB1 mutations are highly prevalent and were detected in 84 to 87% of all sporadic fibromatosis/desmoid tumors. Most CTNNB1 mutations in fibromatosis/desmoid tumors are predominantly missense mutations in codons 41 and 45 of exon 3. These mutations result in β-catenin stabilization, increased nuclear accumulation and activation of the Wnt signaling pathway. Specific CTNNB1 mutations have been reported to predict recurrence in some cases of extra-abdominal and abdominal aggressive fibromatosis. A S45F mutation increased the risk of recurrence significantly.
Mutations in beta catenin (CTNNB1) are seen in about 90% of adamantinomatous craniopharyngiomas and mutations in BRAF (V600E) in papillary craniopharyngiomas. Adamantinomatous and papillary craniopharyngiomas have been shown to carry clonal mutations that are mutually exclusive. These findings indicate that the adamantinomatous and papillary subtypes have distinct molecular underpinnings, each principally driven by mutations in a single well-established oncogene - CTNNB1 in the adamantinomatous form and BRAF in the papillary form, independent of age. This may have implications for the diagnosis and treatment of these tumors.
Somatic mutations of CDKN2A are present in various tumor types, including, squamous cell carcinoma of the lung, clear cell sarcoma, head and neck cancer, melanoma and esophageal cancer. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types.
Somatic mutations of CDKN2A are present in various tumor types, including, squamous cell carcinoma of the larynx, clear cell sarcoma, head and neck cancer, melanoma and esophageal cancer. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types.
Somatic mutations of CDKN2A are present in various tumor types, including, squamous cell carcinoma of the larynx, clear cell sarcoma, head and neck cancer, melanoma and esophageal cancer. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types.
Somatic mutations of CDKN2A are present in various tumor types, including, squamous cell carcinoma of the larynx, clear cell sarcoma, head and neck cancer, melanoma and esophageal cancer, among other cancer types. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types.
ERBB2 (also HER2) is a transmembrane receptor that is a member of the ERBB family of receptor tyrosine kinases. ERBB2 is altered by amplification and/or overexpression in various cancers, most frequently in breast, esophagogastric and endometrial cancers. Somatic mutations in ERBB2 have been identified in a series of tumors including lobular breast, lung adenocarcinoma, and gastric cancers, among others, with recurrent hotspot alterations in both the extracellular and kinase domains. Preclinical and clinical studies have demonstrated that many of these mutations are transforming and sensitive to FDA-approved ERBB targeted therapies, including trastuzumab, ado-trastuzumab emtansine, lapatinib, and pertuzumab. The ERBB2 p.G776delinsVC variant is one of the in-frame insertions in exon 20 of ERBB2 that have been described in lung adenocarcinoma. Overall, in-frame ERRB2 insertions in exon 20 have been reported in approximately 6% of cases of lung adenocarcinoma which are negative for EGFR, KRAS, ALK alterations and these variants are more frequent in patients who were never-smokers. In vitro studies have shown that this specific variant is associated with constitutive kinase activation and is associated with sensitivity to some ERBB2 inhibitors and therefore, it may represent a targetable mutation in some clinical settings. Please refer to clinicaltrials.gov for additional information. Recommend correlation with other clinical and laboratory findings.
EGFR mutations in GBM cluster in the extracellular (EC) domain and include in-frame deletions (such as the common “variant III” del 6-273) and missense mutations (A289V, A289D, T263P, G598V). In vitro and in vivo studies reveal anchorage-independent growth and tumorigenic potential when the A289 and G598 variants are stably expressed in NIH-3T3 cells. The A289 and G598 mutations sensitize Ba/F3 cells to erlotinib in vitro according to some reports, although other reports state glioma-specific EGFR EC mutants are poorly inhibited by EGFR inhibitors that target the active kinase conformation (e.g., erlotinib). The A289 variant has been reported to show sensitivity towards BAY846, a tyrosine kinase inhibitor in brain tumors. In addition, according to some reports, inhibitors which bind to the inactive EGFR conformation potently inhibit EGFR EC mutants and induce cell death in EGFR mutant GBM cells.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to EGFR inhibitors. Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions , EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions , EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M. Erlotinib Afatinib Gefitinib Osimertinib
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions , EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M.
EGFR D770N in Exon 20 has been reported. The significance is unknown.
EGFR exon 20 insertion testing identifies a distinct subset of lung adenocarcinomas, accounting for at least 9% of all EGFR-mutated cases and by molecular modeling, are predicted to have potentially different effects on erlotinib binding. Studies show that in contrast to the more classic activating EGFR mutations, these insertions have been associated with de novo resistance to approved EGFR-TKIs (erlotinib and gefitinib). In a recent study, patients with advanced lung adenocarcinoma harboring exon 20 insertions demonstrated no response or partial response following treatment with TK inhibitors. Exon 20 insertion mutations in EGFR may be associated with clinical trials (https://clinicaltrials.gov/).
EGFR exon 20 insertion testing identifies a distinct subset of lung adenocarcinomas, accounting for at least 9% of all EGFR-mutated cases and by molecular modeling, are predicted to have potentially different effects on erlotinib binding. Studies show that in contrast to the more classic activating EGFR mutations, these insertions have been associated with de novo resistance to approved EGFR-TKIs (erlotinib and gefitinib). In a recent study, patients with advanced lung adenocarcinoma harboring exon 20 insertions demonstrated no response or partial response following treatment with TK inhibitors. This rare complex mutation (p.H773_V774delinsLM) results in the H773L/V774 mutation compound at the same allele, potentially weakening the inactive state and leading to constitutional activation of EGFR. A recent clinical report suggests this mutation is insensitive to the reversible TKI gefitinib, but can be suppressed by the irreversible TKI osimertinib, leading to sustained disease control (Yang et al., Lung Cancer, 121:1-4, 2018). Exon 20 insertion mutations in EGFR may be associated with clinical trials (https://clinicaltrials.gov/).
In GBM, EGFR mutations typically cluster in the extracellular domain and include in-frame deletions (such as the common “variant III” del 6-273) and missense mutations (A289V, A289D, T263P, G598V). EGFR exon 20 insertions have not been previously reported in GBM. The clinical significance of this mutation with regards to response to anti-EGFR therapy in GBM is unknown. In general, EGFR exon 20 mutations have been reported in approximately 9% of all EGFR-mutated cases of lung cancer and studies show that in contrast to the more classic activating EGFR mutations, these insertions have been associated with de novo resistance or only partial response to approved EGFR-TKIs (erlotinib and gefitinib) in lung cancer.
The EGFR D761 mutation is associated with acquired resistance to EGFR-TKIs (Balak et al., 2006). The functional significance of this alteration is being investigated.
A low frequency mutation detected in lung and gastric cancer. Functional significance of this alteration has not yet been described. However, a single NSCLC patient with this mutation in a clinical trial shows partial response to gefitinb therapy
It is unclear what effect the EGFR P753S varaints has on the EGFR protein. However the location of the variant in the splice site acceptor of Exon 19 may activate the kinase domain. The identification of the EGFR P735S mutation in the context of a dramatic response to cetuximab in a patient with cutaneous squamous cell carcinoma, indicates a new potential pairing of EGFR mutation and targeted therapy for patients with cSCC.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions , EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The L861Q mutation is one of the less common mutations which is an activating mutation that is believed to confer sensitivity to the targeted EGFR tyrosine kinase inhibitors although this mutation may confer reduced response to these inhibitors compared to the more common mutations.
Compound (dual) mutations in EGFR have been previously reported in lung adenocarcinoma and typically include a strong activating mutation combined with a weaker activating mutation. These cases appear to respond well to the EGFR targetted therapies if they include mutations that are known to provide sensitivity to EGFR inhibitor therapies. L858R is a well known activating mutation in exon 21 that is associated with sensitivity to EGFR inhibitors. In vitro functional characterization of mutations at E709 have also been reported to be activivating mutations that are also associated with sensitivity to EGFR inhibitors in vitro. Mutations in E709 often occur together with other muations in EGFR including the L858R mutation.
In GBM, EGFR mutations typically cluster in the extracellular domain and include in-frame deletions (such as the common “variant III” del 6-273) and missense mutations (A289V, A289D, T263P, G598V). However, the p.E709K mutation in the tyrosine kinase domain of EGFR has not been previously reported in GBM. In vitro functional characterization of mutations at E709 have been reported to be activivating mutations that are associated with sensitivity to EGFR inhibitors in vitro in some cell systems. The clinical significance of this mutation with regards to response to anti-EGFR therapy in GBM is unknown.
FBXW7 is a tumor suppressor gene that is mutated in several tumors including colorectal, liver, bladders and ovarian cancers. It is also mutated in endometrial and head and neck squamous cancers. Preclinical data suggest that FBXW7 mutations may sensitize cells to mTOR inhibitors.
FBXW7 is a tumor suppressor gene and is responsible for ubiquitination and turnover of several oncoprotiens. Loss-of-function mutations of FBXW7 lead to constitutive NOTCH1 pathway activation via inhibition of ubiquitin-mediated degradation of activated NOTCH1 and MYC. FBXW7 mutations have been reported in ~3-8% of melanomas. Preclinical data suggest that FBXW7 mutations sensitize cells to mTOR inhibitors. However, advanced tumors with somatic FBXW7 mutations and other concurrent molecular alterations might have limited therapeutic response to mTOR inihibitors. Correlation with other clinical and laboratory findings is recommended.
FGFR3 has been found to be mutated in up to 64% of cases of bladder cancer; FGFR3 mutations tend to be exclusive of RAS mutations ,TP53 overexpression, TP53 mutation, but not PIK3CA mutations. However, subsets of cases with co-mutations have been described. FGFR3 mutations (including Y373C) are believed to lead to constitutive activation of the receptor and activation of the RAS-MAPK pathway. FGFR3 mutations are often seen in non-muscle invasive bladder cancers and tend to correlate with low stage and grade; however FGFR3 mutations have also been described in muscle-invasive bladder cancer. Targeted therapies with FGFR3 inhibitors have been explored in patients with bladder cancer.
This GNAS mutation causes constitutive activation of the G-protein complex and activates adenylate cyclase to produce cyclic-AMP (cAMP) that can activate oncogenic pathways. The R201 mutation in GNAS was thought to both drive tumor progression and confer exceptional chemo-sensitivity in a patient with an unclassified kidney cancer.
When mutated, HRAS can act as an oncogene, causing normal cells to become cancerous. Somatic HRAS mutations have been associated with some cases of bladder, thyroid and kidney cancers and in nevi. Based on clinical evidence in melanoma with the related family member NRAS, downstream pathway MEK inhibitors may be a feasible treatment strategy. The effectiveness of MEK inhibitors for HRAS-mutant thyroid and bladder cancer patients has not yet been investigated.
RAS is a family of small GTPases and acts as an oncogene. Point mutations in codons 12 and 13 of RAS gene increases its affinity for GTP and those in codon 61 inactivate its autocatalytic GTPase function, resulting in permanent RAS activation and stimulation of its downstream targets along the MAPK and PI3K/AKT signaling pathways. In thyroid, RAS (HRAS, NRAS and KRAS) mutations are identified in 10--20% of papillary carcinomas, 40--50% of follicular carcinomas, 10% of medullary carcinomas, and 20--40% of poorly differentiated and anaplastic carcinomas. The frequency of HRAS mutations in thyroid carcinomas is approximately 4%. HRAS mutations at codon 61 have been reported in a variety of thyroid lesions and are especially prevalent in the follicular variant of papillary thyroid carcinoma. However, the predictive or prognostic significance of HRAS mutation in thyroid carcinoma is not clear and correlation with other clinical and laboratory findings is necessary.
When mutated, HRAS can act as an oncogene. Somatic HRAS mutations have been associated with some cases of upper and lower urinary tract urothelial carcinoma, thyroid, and kidney cancers and in nevi. The frequency of HRAS mutations in upper and lower urinary tract urothelial carcinoma are about 10%. Interestingly, it has been shown that the HRAS mutation in lower urinary tract urothelial carcinoma may occur in tumors without FGFR3 mutations.
IDH1 or IDH2 mutations are found in >70% of lower grade diffusely infiltrative gliomas and in >90% of secondary glioblastoma. IDH mutational status has been reported to be a favorable prognostic indicator relative to wild-type gliomas of similar histology, regardless of grade. Therapeutic strategies exploiting mutated IDH protein, including through direct inhibition and vaccine-based approaches, are currently the subject of preclinical research and clinical trials.
IDH-mutant tumors have aberrant production and accumulation of the oncometabolite 2-hydroxyglutarate (2-HG), which may play a pivotal oncogenic role in several malignancies. A case of an IDH1 p.R132L mutation in a patient with hormone receptor-positive (HR+) breast adenocarcinoma has been reported (5). IDH1 mutations may impact a rare subgroup of patients with breast adenocarcinoma, suggesting future avenues for disease monitoring through noninvasive measurement of 2-HG, as well as for the development and study of targeted therapies against the aberrant IDH1 enzyme.
IDH-mutant tumors have aberrant production and accumulation of the oncometabolite 2-hydroxyglutarate (2-HG), which may play a pivotal oncogenic role in several malignancies including AML, central nervous system and billary tract. Strikingly, IDH1 mutations were rarely detected in the other solid tumor types. Reports have shown that melanoma cases can harbor IDH1 mutations. An IDH1 R132C mutation was found in a melanoma metastasis to the lung. IDH1 mutations were found to coexist with BRAF or KIT mutations, and all were detected in metastatic lesions. Coexistence of IDH1 R132C mutation with KRAS has also been reported in a single case of lung adenocarcinoma (Sequist et al., Ann Oncol., 22:2616-2624, 2011). The clinical significance of this mutation with regards to response to anti-IDH1 therapy in lung cancer is unknown.
Reports have shown that melanoma cases can harbor IDH1 mutations. An IDH1 R132C mutation was found in a melanoma metastasis to the lung. IDH1 mutations were found to coexist with BRAF or KIT mutation, and all IDH1 mutations were detected in metastatic lesions. BRAF-mutated melanoma cells, additionally expressing the cancer-related IDH1 mutant have been shown to have increased colony-forming and in vivo growth activities.
IDH1 or IDH2 mutations are found in >70% of lower grade diffusely infiltrative gliomas and in >90% of secondary glioblastoma. IDH mutational status has been reported to be a favorable prognostic indicator relative to wild-type gliomas of similar histology, regardless of grade. Therapeutic strategies exploiting mutated IDH protein, including through direct inhibition and vaccine-based approaches, are currently the subject of preclinical research and clinical trials.
The M541L mutation has been implicated in hematological malignancies. It may help to identify a subgroup of cases who may benefit from low dose imatinib therapy. KIT mutations are also associated with Gastro Intestinal Stromal Tumors. The KIT variant M541L was originally thought to be associated with increased risk of certain tumors such as aggressive fibromatosis (AF; Dufresne et al., 2010). However, larger scale studies have shown that the prevalence of this mutation within AF does not differ from that of the general population and this variant was not found to be tumor-specific, classifying it as a single nucleotide polymorphism and non-pathogenic (Grabellus et al., 2011).
Approximately 50-60% of the oncogenic mutations in Gastrointestinal stromal tumors (GIST) are present in Exon 11 of the KIT gene. The E554K variant is present in Exon 11 of the KIT gene. Identification of GIST genotype is important given the availability of targeted therapy with KIT/PDGFRA tyrosine kinase inhibitors (eg, imatinib, sunitinib, etc).
KIT mutations occur in approximately 80% of patients with gastrointestinal stromal tumors. The major region of KIT mutation in GIST is within exon 11, occurring in about 65% of patients. KIT exon 11 mutations are activating mutations and are typically sensitive to treatment with Imatinib.
KIT mutations occur in approximately 15-20% of patients with mucosal melanomas. The majority ofKIT mutations occur within exon 11 and they are less frequent in other exons. The N822K mutation in exon 17 occurs within the kinase domain of KIT. Mutant KIT proteins have increased kinase activity and transforming activity in vitro. Although KIT activating mutations in exons 11 and 13 are typically sensitive to treatment with Imatinib, there was no response to treatment noted in patients harboring mutations in exon 17 (Ref. 4).
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. Such mutations are found in approximately 30% to 50% of metastatic colorectal tumors and are common in other tumor types. Mutations in the KRAS gene may indicate poor prognosis and poor drug response with therapies targeted to EGFR. The absence of a KRAS mutation predicts a greater likelihood of response to EGFR-targeted therapies and improved survival with such treatment. The relevant KRAS mutation is in one of five codons (12 13, 61, 117 or 146). The presence of KRAS mutations in codon 12, 13 or 61 is associated with a high likelihood of resistance to therapies targeting EGFR. In addition, mutations at codons 117 and 146 may also be associated with reduced response to EGFR-targeted therapies. Results should be interpreted in conjunction with other laboratory and clinical findings. Drug resistance: Panitumumab Cetuximab
KRAS belongs to the RAS family of oncogenes. In lung, KRAS mutations are detected in approximately 20% to 25% of adenocarcinoma and less than 10% of squamous cell carcinoma which demonstrate a minor glandular component. KRAS mutations in NSCLC most often occur in codons 12 or 13 and with a lower frequency in codon 61. Mutations in KRAS are usually mutually exclusive with other oncogenic driver aberrations including EGFR, BRAF, HER2 mutations and ALK and ROS1 rearrangements. Contrary to most other oncogenic driver mutations, KRAS is more often found in smokers and is detected at lower frequency in East Asian patient cohorts. The prognostic as well as predictive role of KRAS mutations continues to be studied. Although various attempts inhibiting KRAS have been made, there is no established therapy specific for this large patient subpopulation. Recommend correlation with other clinical and lab findings.
KRAS belongs to the RAS family of oncogenes. KRAS mutations are detected in approximately 20% to 25% of lung adenocarcinoma. Contrary to most other oncogenic driver mutations, KRAS is more often found in smokers and is detected at lower frequency in East Asian patient cohorts. Mutations in KRAS are usually mutually exclusive with other oncogenic driver aberrations including EGFR, BRAF, HER2 mutations and ALK and ROS1 rearrangements. KRAS mutations in NSCLC most often occur in codons 12 or 13 and with a lower frequency in codon 61. The prognostic as well as predictive role of KRAS mutations continues to be studied. Although various attempts inhibiting KRAS have been made, there is no established therapy specific for this large patient subpopulation.
Pancreatic ductal adenocarcinoma (PDAC) is initiated by oncogenic mutant KRAS, which has been shown to drive pancreatic neoplasia. More than 90% of pancreatic ductal adenocarcinoma samples have a KRAS mutation which may have prognostic, and (with ongoing trials assessing the efficacy of novel KRAS inhibitors) possibly therapeutic implications. However, targeting KRAS directly has been difficult in these tumors.
KRAS belongs to the RAS family of oncogenes. KRAS mutations have been described in approximately 3-40% gall bladder adenocarcinomas (more often in East Asia). The prognostic and therapeutic implications of KRAS mutations in gall bladder adenocarcinomas continue to be explored.
Activating somatic mutations in the tyrosine kinase domain of MET are found in about 10-15% of sporadic papillary renal cell carcinoma (pRCC). MET mutations are predominantly associated with Type 1 pRCC tumors. The responses to foretanib an oral inhibitor of MET and other tyrosine kinases including VEGFR2, have been described in patients with papillary renal cell cancer.
Nonsynonymous mutations in the MET gene have been described in non-small cell lung cancer (NSCLC) and (small cell lung cancer) SCLC. Increased expression of MET protein was associated with improved progression free survival and overall survival in patients who received MetMAb (an anti-MET antibody) and erlotinib. The activity of MET inhibitors in NSCLC or SCLC tumors with non-kinase domain MET mutations is not yet known.
The MET p. E168D mutation has been reported in various tumors including lung cancer according to the COSMIC database. Some studies indicate that this mutation may be associated with higher affinity for ligand, HGF. In vitro studies in cell lines with cells expressing MET p.E168D may show increased sensitivity to MET inhibitor. According to ClinVar, this particular variant is a likely benign germline variant (https://preview.ncbi.nlm.nih.gov/clinvar/variation/41627/). The clinical significance of this variant remains to be fully elucidated.
The MET p.T1010I variant has been reported in some tumor types and also has been reported as a germline variant present in less than 1% of the general population. Its role in tumor development and progression continues to be studied. The utility of MET pathway inhibitors also continues to be explored.
A subset of sporadic papillary renal carcinomas were caused by activating mutations in the tyrosine kinase domain of the MET proto-oncogene. Several of the MET mutations (M1268T, D1246 and V11101) were located in codons homologous to codons mutated in other protein receptor tyrosine kinases (Ret M918T, Kit D816V, and c-erbB V1571)
The MLH1 V384D polymorphism has been associated with cancer risk in some tumor types. In addition, according to one report, MLH1 V384D polymorphism has been reported to be associated with primary resistance to EGFR-TKIs in patients with EGFR L858R-positive lung adenocarcinoma and may potentially be a novel biomarker to guide treatment decisions for those patients. The effect of this MLH1 polymorphism when present with other EGFR-TKI sensitizing mutations such as Exon 19 deletions in EGFR remains to be clarified. Some studies have shown that patients carrying the MLH1 V384D variant have an increased risk of the development of microsatellite-instable as well as -stable colorectal cancer. This variant has an allele frequency of 4% in the East Asian population. Of note, this variant is reported as a benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/41632/). Clinical correlation is recommended.
NRAS mutations occur in approximately 1--6% of colorectal cancers. Several studies have shown that patients with NRAS-mutated tumors are less likely to respond to cetuximab or panitumumab, but this may not have an effect on PFS or overall survival.
Somatic mutations in NRAS have been found in approximately 13-25% of all malignant melanomas. The result of these mutations is constitutive activation of NRAS signaling pathways. NRAS mutations are found in all melanoma subtypes, but may be slightly more common in melanomas derived from chronic sun-damaged (CSD) skin . Currently, there are no direct anti-NRAS therapies available.
RAS mutations (HRAS, NRAS and KRAS) are found in all epithelial thyroid malignancies. The frequency of HRAS mutations in thyroid carcinomas is 4%. RAS mutations are identified in 10-20% of papillary carcinomas, 40-50% of follicular carcinomas and 20-40% of poorly differentiated and anaplastic carcinomas .
NRAS gene belongs to the family of RAS genes. It encodes a G protein that is important in the transmission of growth-promoting signals from the cell surface receptors to the nucleus through RAS-RAF- mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)-AKT cell signaling pathways. NRAS mutations are the most common type of RAS mutations in thyroid nodules. Activating point mutations in NRAS gene have been associated with follicular-patterned neoplasms including follicular adenoma, follicular carcinoma and follicular variant papillary thyroid carcinoma cases. NRAS mutations have been also detected in a subset of poorly differentiated carcinoma and anaplastic carcinoma. NRAS mutations concentrate in codon 61, while those in codons 12 or 13 are rare. According to some studies, there is a significant correlation between RAS mutations and distant bone metastases among follicular and papillary carcinomas. However, RAS mutations are also frequently found in encapsulated follicular variant of papillary carcinoma, a tumor with an indolent behavior. Clinical correlation is recommended.
RAS mutations have also been identified in benign Follicular Adenomas(FA); however, it is unclear whether RAS positive FA have a higher chance of progression to cancer. The prevalence of this mutation in benign thyroid nodules is between 20 and 40%. The low overall prevalence of RAS mutations in thyroid cancers and the relatively high mutation rate in benign nodules makes ras mutation analysis unsuitable as a standalone test to predict malignancy in indeterminate thyroid nodules.
NRAS is a member of the RAS family of oncogenes and activating mutations of NRAS have been reported in about 1% of NSCLCs and are mostly exclusive of other known driver mutations. The Q61 codon is most frequently affected. In preclinical studies, cell lines harboring NRAS mutation(s) showed variable sensitivities to pathway inhibitors.
NRAS is a member of the RAS family of oncogenes and activating mutations of NRAS have been reported in a wide variety of tumors including occasional cases of cholangiocarcinomas.
NRAS is a member of the RAS family of oncogenes and activating mutations of NRAS have been reported in a wide variety of tumors including occasional cases of bladder cancer. This finding may influence targeted therapy options.
The D842V mutation results in an amino acid substitution at position 842 in PDGFRA, from an aspartic acid (D) to a valine (V). This mutation occurs within the TK2 domain. PDGFRA D842V mutation has been found in a distinct subset of GIST, typically from the stomach. The D842V mutation is known to be associated with tyrosine kinase inhibitor resistance. Recent evidence has shown that Dasatinib has been also recently associated with promising clinical activity in patients with advanced GIST carrying exon 18 mutation of the PDGFRA gene (including the D842V mutation). Interestingly, recent in vitro data have suggested that crenolanib, a highly selective and potent inhibitor of both PDGFRA and PDGFRB, blocks phosphorylation of D842V mutant PDGFRA at clinically achievable concentrations
PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways.The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains), with 80% of the identified mutations found within three hotspot: E542K, E545K, and H1047R. PIK3CA mutations are often found in hormone receptor positive breast cancer and have been associated with resistance to anti-EGFR therapy in some studies but not in others.
Somatic mutations in PIK3CA have been found in 10-30% of colorectal cancers. According to some reports, co-occurrence of both exon 9 and exon 20 PIK3CA mutations, when present, may be associated with a poor prognosis. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use is associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation may be a molecular biomarker that predicts response to aspirin therapy. PIK3CA may also be a target of directed therapy in some clinical settings.
Somatic mutations in PIK3CA are seen in approximately 2% of papillary thyroid carcinoma, poorly differentiated carcinoma, anaplastic carcinoma. Somatic mutations of PIK3CA have been described particularly in advanced and dedifferentiating thyroid tumors. Their prevalence varies from 16 to 23% in anaplastic thyroid carcinomas. They are less frequent in papillary and follicular thyroid carcinomas and the prevalence in medullary thyroid carcinomas remains unknown. Although inhibitors of the PI3K/AKT/mTOR pathway have shown efficacy against thyroid cancer in pre-clinical models, their success in clinical trials remains to be determined.
PIK3CA mutations have been identified in pediatric and adult gliomas including: anaplastic oligodendrogliomas, anaplastic astrocytomas, glioblastoma multiforme, rosette forming glioneuronal tumors and medulloblastomas. PIK3CA mutations provide a mechanism for disrupting the PI3K/Akt pathway.
Somatic mutations in PIK3CA have been found in 1–3% of NSCLC. These mutations typically occur within specific hotspot regions. PIK3CA mutations appear to be more common in squamous cell histology compared to adenocarcinoma and can occur with or without a history of smoking. PIK3CA mutations can co-occur with EGFR mutations and PIK3CA mutations have been detected in a small percentage (approximately 5%) of EGFR-mutated lung cancers with acquired resistance to EGFR TKI therapy.
IDH-mutant tumors have aberrant production and accumulation of the oncometabolite 2-hydroxyglutarate (2-HG), which may play a pivotal oncogenic role in several malignancies. Mutations in IDH1 and IDH2 have been reported in intrahepatic cholangiocarcinomas. IDH1 mutation has been associated with highly elevated tissue levels of the enzymatic product 2-hydroxyglutarate. IDH1 mutation has been described to be a feature of intrahepatic cholangiocarcinomas.
When mutated, HRAS can act as an oncogene, causing normal cells to become cancerous. Somatic HRAS mutations have been associated with some cases of bladder, thyroid and kidney cancers and in nevi. HRAS mutations are rarely found in the breast and the HRAS Q61R mutation has not been previously reported in this cancer. Inferring the clinical evidence seen in melanoma, downstream pathway MEK inhibitors may be a feasible treatment strategy. The effectiveness of MEK inhibitors for HRAS-mutant thyroid and bladder cancer patients has not yet been investigated.
MET is a member of the receptor tyrosine kinase and proto-oncogene playing a major role in tumor development and metastasis. MET E168D has been previously reported in papillary thyroid carcinoma. This mutation is located in the SEMA domain containing the ligand binding site. In vitro study has shown that E168D alters MET functionality in lung cancer. The prognostic and predictive significance of MET mutations in thyroid cancer is not clear and correlation with other clinical and laboratory findings is necessary. Of note, this variant is reported as a likely benign germline variant in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/41627/).
PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways.The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains). Activating mutations in PIK3CA are found are found in a wide variety of human cancers including 27% urothelial bladder cancers, with a higher prevalence in low grade tumors. Up to 13.6% of renal pelvic urothelial carcinomas also harbor activating somatic mutations in PIK3CA gene. The role of PIK3CA mutations as prognosticators of outcome or predictors of therapeutic response awaits further evaluation.
PTEN mutations occur in 5-14% of colorectal cancers. PTEN is a tumor suppressor gene, and loss of PTEN results in upregulation of the PI3K/ AKT pathway. PTEN loss of expression is observed with KRAS, BRAF, and PIK3CA mutations. In retrospective studies, PTEN loss is associated with decreased sensitivity of colorectal cancer tumors to anti-EGFR antibodies. PTEN loss is associated with lack of benefit of the anti-EGFR antibody, cetuximab.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is mutated in a large number of cancers. It encodes a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Cancer-associated alterations in this gene often result in loss of PTEN protein and upregulation of the PI3K/AKT/mTOR pathway. PTEN mutations have been reported in 15% of anaplastic thyroid cancer. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome. Patients with Cowden syndrome have an increased risk of developing epithelial thyroid cancer, follicular carcinoma being the most common, of up to 10% compared to <1% in the general population. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.
Somatic mutations in PTEN have been found in 4-8% of non-small cell carcinomas (NSCLC) including adenocarcinomas and squamous cell carcinomas. PTEN is a tumor suppressor gene, and loss of PTEN results in upregulation of the PI3K/ AKT pathway. Loss of PTEN is most commonly due to promoter hypermethylation, while homozygous deletion and nonsense mutations with loss of heterozygosity (LOH) may also occur. PTEN mutations may occur in multiple exons. In preclinical studies, PTEN loss is associated with decreased sensitivity of EGFR mutant lung tumors to EGFR TKIs. Clinical trials assessing the efficacy of PI3K inhibitors in PTEN loss are being explored.
The RB1 protein is a negative regulator of the cell cycle and was the first tumor suppressor gene found. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Defects in this gene are a cause of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic sarcoma - See more at: http://www.cancerindex.org/geneweb/RB1.htm#sthash.uzBqWCrJ.dpuf
Colorectal cancers (CRCs) frequently harbor somatic mutations in the pathway members SMAD4. The prevalence of SMAD4, SMAD2, and SMAD3 mutations in sporadic CRCs was 8.6% (64 of 744), 3.4% (25 of 744), and 4.3% (32 of 744), respectively. Somatic SMAD4 mutations have been reported to be more common in advanced stages of CRCs and LOH at the SMAD4 locus has been associated with poor prognosis. SMAD4 mutations were associated with mucinous histology.
SMAD4 is a tumor suppressor gene that is mutated in one third of colorectal cancer and half of pancreatic tumors. SMAD4 inactivation by allelic deletion or mutation mainly occurs in late stage pancreatic ductal adenocarcinoma and is associated with poorer prognosis. SMAD4 loss increased resistance to the chemotherapeutic agent 5'-fluorouracil.
Homozygous mutations causing SMAD4 loss are found in approximately 3% of lung adenocarcinomas and squamous cell carcinomas cases. SMAD4 loss tends to act synergistically with TP53 and KRAS mutations to increase lymphatic metastasis and tumor size. Experimental work in a mouse model has demonstrated increased susceptibility to DNA topoisomerase inhibitors with homozygous SMAD4 loss of function mutation coupled with KRAS G12D activating mutations.
Based on reports in the literature, EGFR and KRAS mutations can occasionally coexist in the same bronchial-pulmonary carcinoma. The biological implications of this coexistence are still poorly understood mainly because these cases are not frequent. It is therefore necessary to study larger series of cases with the two mutations to better understand the biological, clinical and therapeutic implications. Patients with coexisting EGFR and KRAS variants may have a partial response to EGFR TKI.
ERBB2 V842I is a mutation identified in breast cancer patients, located within the kinase domain, which increases kinase activity, in vitro, and increases the number of colonies formed in soft agar. Cells with this mutation display an invasive morphology, but tumor xenografts formed from these cells do not grow more rapidly than those with wild-type HER2. When assessing sensitization to HER2-targeted therapies in vitro, cells with this mutation are highly sensitive to neratinib but less sensitive to lapatinib, in a manner similar to wild-type HER2.
Greater than 40% of glioblastomas (GBM) harbor focal amplification of the EGFR locus and there is evidence to suggest that these are driver alterations in these patients, making the EGFR pathway a potential therapeutic target in some clinical settings. Moreover, this alteration is relatively specific for GBM with very few other diffusely infiltrative gliomas having been shown to carry focal amplification of this locus (<3%). In GBM, this alteration frequently occurs in combination with other alterations of EGFR including polysomy 7, intragenic inframe deletions (e.g. EGFRvIII), and/or somatic point mutations. Based on current evidence, the independent predictive value of EGFR amplification in GBM is unclear. The relationship between individual and concurrent EGFR alterations and clinical response to small molecular inhibitors targeting EGFR is currently under investigation in clinical trials.
NOTCH2 gain of function mutations have been reported in approximately 25% of splenic marginal zone lymphomas and are thought to be rare in non-splenic marginal zone lymphomas. These mutations are typically located near the C-terminal PEST domain and lead to protein truncation or, more rarely, are nonsynonymous substitution mutations affecting the extracellular heterodimerization domain. In addition, NOTCH2 PEST domain mutations have been reported in approximately 8% of diffuse large B cell lymphomas and in vitro systems suggest that PEST domain mutant NOTCH2 receptors have increased activity compared to wild type NOTCH2. The prognostic and therapeutic implications of these alterations continue to be elucidated.
MDM2 encodes an E3 ubiquitin ligase that regulates tumor suppressor protein (eg, TP53) turnover through proteasomal degradation. MDM2 overexpression or amplification has been detected in a variety of different cancers including a subset of bladder cancer. Small molecular inhibitors of the MDM2:p53 axis are currently in early phase clinical trials for a number of malignancies.
Recurrent inactivating mutations in Kruppel-like factor 2 (KLF2),have been reported in approximately 40% of splenic marginal zone lymphomas (SMZL) but are rarely present in other B-cell lymphomas, according to one study. The majority of KLF2 mutations were frameshift indels or nonsense changes, with missense mutations clustered in the C-terminal zinc finger domains. Functional assays showed that these mutations inactivated the ability of KLF2 to suppress NF-κB activation. IGHV1-2 rearrangement and 7q deletion were primarily seen in SMZL with KLF2 mutation, while MYD88 and TP53 mutations were nearly exclusively found in those without KLF2 mutation. NOTCH2, TRAF3, TNFAIP3 and CARD11 mutations were observed in SMZL both with and without KLF2 mutation. The prognostic and therapeutic implications, if any, of KLF2 alterations in SMZL has yet to be fully elucidated.
JAK3 is a non-receptor protein tyrosine kinase involved in the interferon-alpha/beta/gamma pathway and is a member of the JAK/STAT signaling pathway. The JAK3 V722I variant has been reported as a likely benign germline polymorphism (ClinVar, https://preview.ncbi.nlm.nih.gov/clinvar/variation/134573/) and also as an acquired somatic variant in some tumors. It has been reported to be an activating variant of JAK3 and initial in vitro studies suggest that this variant may play a role in the regulation of PD-L1 expression. Also, V722I resulted in constitutive phosphorylation of Jak3 and was transforming in cell culture. Clinical correlation is recommended.
Somatic mutations in TP53 are frequent in human cancer. Germline TP53 mutations cause of Li-Fraumeni syndrome, which is associated with a range of early-onset cancers. The types and positions of TP53 mutations are diverse. TP53 mutations may be potential prognostic and predictive markers in some tumor types, as well as targets for pharmacological intervention in some clinical settings. The IARC TP53 Database (http://www-p53.iarc.fr/) is a useful resource which catalogues TP53 mutations found in cancer.
Somatic mutations in TP53 are frequent in human cancer. Germline TP53 mutations cause of Li-Fraumeni syndrome, which is associated with a range of early-onset cancers. The types and positions of TP53 mutations are diverse. TP53 mutations may be potential prognostic and predictive markers in some tumor types, as well as targets for pharmacological intervention in some clinical settings. The IARC TP53 Database (http://www-p53.iarc.fr/) is a useful resource which catalogues TP53 mutations found in cancer.
Somatic mutations in TP53 are frequent in human cancer. Germline TP53 mutations cause of Li-Fraumeni syndrome, which is associated with a range of early-onset cancers. The types and positions of TP53 mutations are diverse. TP53 mutations may be potential prognostic and predictive markers in some tumor types, as well as targets for pharmacological intervention in some clinical settings. The IARC TP53 Database (http://www-p53.iarc.fr/) is a useful resource which catalogues TP53 mutations found in cancer.
Somatic mutations in TP53 are frequent in human cancer. Germline TP53 mutations cause of Li-Fraumeni syndrome, which is associated with a range of early-onset cancers. The types and positions of TP53 mutations are diverse. TP53 mutations may be potential prognostic and predictive markers in some tumor types, as well as targets for pharmacological intervention in some clinical settings. The IARC TP53 Database (http://www-p53.iarc.fr/) is a useful resource which catalogues TP53 mutations found in cancer.
KDM5C (JARID1C) encodes a histone demethylase that is involved in the regulation of transcription and chromatin remodeling. Mutations in KDM5C are noted in about 8% of clear cell renal cancers, and are associated with advanced stage, grade and tumor invasiveness. However, KDM5C- mutated metastatic renal cell cancer are associated with an improved progression free survival in response to sunitinib.
SETD2 protein is a histone H3 lysine 36 trimethylating (H3K36Me3) enzyme affecting chromatin accessibility and DNA methylation. In addition, SETD2 plays an important role in DNA damage repair through promoting homologous recombination, mismatch repair, and activation of p53-mediated checkpoints. SETD2 gene is mutated in 10–15% of ccRCC tumors. Mutational analyses indicate that SETD2 mutations tended to be subclonal, and are thought to be associated with advanced tumor stage at presentation and a higher rate of metastatic disease, as well as decreased survival. Furthermore, SETD2 mutations occur more frequently when PBRM1 is mutated, suggesting that these mutations could be cooperating with each other.
BAP1 (BRCA1 associated protein-1) is a histone deubiquitinase, with the ubiquitin C-terminal hydrolase (UCH) domain located at its N-terminal domain. This gene is thought to be a tumor suppressor gene that functions in the BRCA1 growth control pathway. Inactivating mutations of the BAP1 gene have been reported in 10–15% of ccRCCs. In addition to a potentially critical role for BAP1 inactivation in epigenetic deregulation in ccRCC, BAP1 has been found to promote DNA double-strand break repair by homologous recombination, thereby adding to its tumor suppressor function. Multiple studies have revealed that, in a substantial portion of ccRCC tumors with BAP1 mutations, the mutations are subclonal and the protein losses are focal. Interestingly, in ccRCC tumors, the mutations of BAP1 and PBRM1 are largely mutually exclusive. BAP1 protein loss has been associated with advanced clinical stage, higher tumor grade, shorter median survival, worse cancer-specific survival and advanced clinical stage.
PBRM1 is second most commonly mutated gene (35%) in primary clear cell renal cell carcinoma after VHL. This locus encodes a subunit of ATP-dependent chromatin-remodeling complexes. The encoded protein has been identified as in integral component of complexes necessary for ligand-dependent transcriptional activation by nuclear hormone receptors. PBRM1 is likely a tumor suppressor because the reported mutations are mostly inactivating truncations. PBRM1 mutations, similar to those of VHL, occur early in ccRCC tumorigenesis, with mutations being present in all cancer cells within a tumor in many cases. The contribution of PBRM1 mutations to the clinical outcome of ccRCC patients has been controversial. Some groups reported that these mutations did not seem to correlate with adverse patient survival. However, other groups have reported that PBRM1mutations are positively linked to tumor invasiveness and, based on immunohistochemistry findings, loss of the PBRM1 protein was associated with advanced tumor stage, high Fuhrman grade, and poor overall survival.
The Von Hippel-Lindau (vHL) gene may be altered as a somatic (acquired) alteration and/or as a germline alteration associated with a rare autosomal dominant inherited cancer syndrome predisposing to a variety of malignant and benign tumors including clear cell renal cell carcinoma (ccRCC). The protein encoded by this gene is involved in the ubiquitination and degradation of hypoxia-inducible-factor (HIF), which is a transcription factor that plays a central role in the regulation of gene expression by oxygen. Biallelic VHL gene defects (truncation and missense) occur in approximately 75% of ccRCC cases. In addition, approximately 19% of tumors show evidence of inactivation by methylation of the VHL gene promoter. Studies of VHL mutational status as a prognostic marker in advanced sporadic RCC have been inconsistent. However, recent studies with VEGF-inhibitors suggested that loss of function mutations in VHL were associated with treatment response. There are ongoing clinical trials using the current VEGF-tyrosine kinase inhibitors specifically in patients with vHL. Correlation with clinical findings and genetic counseling may be helpful if there is clinical concern for an inherited cancer syndrome. Germline variants are not reported as part of the analysis for the whole exome sequencing assay for tumors.
KDM6A (UTX) encodes a histone demethylase enzyme. In vitro and in vivo experiments examining KDM6A depletion and overexpression in bladder tumor cells support a role for KDM6A as a suppressor of tumor growth and cell migration. It is found to be mutated at a low frequency in ccRCC tumors (1%). How KDM6A inactivation contributes to ccRCC tumor biology remains to be determined.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is mutated in a large number of cancers. It encodes a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. PTEN mutations are loss-of-function mutations and occur in 1% to 5% of ccRCCs. Recent studies suggest that only biallelic loss, resulting from deletion and/or inactivating mutations, is associated with an adverse outcome in ccRCCs. Whether PTEN alterations predict for responsiveness to mTORC1 inhibitors is less certain at this time.
FLCN gene mutations cause Birt-Hogg-Dubé (BHD), a hereditary renal cancer syndrome. A classic triad of findings characterizes BHD, which includes cutaneous fibrofolliculomas, pulmonary cysts, and renal tumors. The condition is caused by germline mutations in the FLCN gene, which encodes folliculin; the function of this protein is largely unknown, although FLCN has been linked to the mTOR pathway. Somatic second-hit mutations identified in BHD-associated renal tumours are consistent with a tumour-suppressor function for FLCN. Individuals with BHD have about a 34% lifetime risk for renal cancer, most frequently diagnosed in the fifties. Additionally, male FLCN mutation carriers are twice as likely to be affected as female carriers. Approximately 50% of BHD-related renal tumors manifest as a chromophobe/oncocytic hybrid: 34% chromophobe, 9% clear cell, 5% oncocytoma, and 2% papillary.
Amplification of FGFR1 has been reported in less than 5% of cases of pancreatic adenocarcinoma. Sequence analysis has demonstrated an activating KRAS mutation (exon 2) in all FGFR1-amplified cases according to one study. In vitro studies suggest that proliferation of a cell line with FGFR1 amplification may be inhibited using the FGFR1 inhibitor BGJ398. In the proper clinical context, FGFR1 may represent a potential new therapeutic target in a subset of patients harbouring FGFR1-amplified tumours, however, further study is required.
SPOP (Speckle-type POZ protein) encodes a Cullin 3-based E3-ubiquitin ligase that has several substrates, including the androgen receptor (AR), and steroid receptor coactivator 3 (SRC-3). Upon SPOP mutation in prostate cancer, impaired ubiquitination of its substrates can lead to enhanced AR signaling and cell proliferation. Both AR and AR coactivators are substrates deregulated by SPOP mutation, providing a possible explanation for the associated increase in AR activity seen in this subtype of prostate cancers. SPOP mutations exclusively occur in ETS-negative group of prostate cancer. ERG ubiquitination is also regulated by SPOP. ERG fusion proteins evade SPOP-mediated degradation. This might explain the reason for mutual exclusivity of ETS fusion and SPOP mutation in prostate cancer and create a potential novel therapeutic avenue for ETS fusion tumors. SPOP mutant are significantly associated with CHD1 deletions at 5q21 or 6q21 regions. CHD1 gene controls the transcriptional activity across the genome. It is recurrently deleted in 10%-25% of primary and metastatic prostate cancer, and particularly focal homozygous deletions are restricted to ETS-negative tumors. The SPOP-mutant/CHD1-deleted subset of prostate cancer have characteristic molecular features, including high levels of DNA methylation, homogeneous gene expression patterns, distinct somatic copy-number alterations (SCNA), as well as frequent overexpression of SPINK1 mRNA. The latter is associated with aggressive disease and increased risk of biochemical recurrence. The SPINK1 may act through EGFR pathway, hence, EGFR inhibitors may have therapeutic role in SPINK1-postive prostate cancer.
The ERBB2 p.V842I mutation has been previously reported in several cancer types and has been reported to be an activating mutation. The potential for these mutations to be used for selection of patients to targeted therapies continues to be evaluated.
Beta catenin is a transcriptional co-regulator and an adapter protein for cellular adhesion; it comprises part of the Wnt signaling pathway and intracellular levels of beta-catenin are regulated by its phosphorylation, ubiquitination and proteosomal degradation. Accumulation of nuclear beta catenin can lead to a tumoral phenotype and oncogenic transformation in a variety of solid tumors. Various oncogenic mutants of beta catenin have been found in different tumor types which alter its degradation, leading to its accumulation and promoting tumor growth. Mutations in exon 3 of CTNNB1 result in stabilization of a protein that resists degradation, leading to nuclear accumulation of b-catenin, have been described in endometrioid endometrial carcinoma. The reported frequency of CTNNB1 mutations in endometrioid endometrial carcinoma ranges from 14-44%. However, these mutations are not described previously in endometrial sarcomas. Of note, CTNNB1 mutations are highly common in desmoid fibromatosis.
CHD1 (chromodomain helicase DNA protein binding domain 1) gene controls the transcriptional activity across the genome. It is recurrently deleted in 10%-25% of primary and metastatic prostate cancer, and particularly focal homozygous deletions are restricted to ETS-negative tumors. CHD1 deletion may contribute to the distinctive patterns of genomic instability observed in CHD1del tumors.The SPOP-mutant/CHD1-deleted subset of prostate cancer have characteristic molecular features, including high levels of DNA methylation, homogeneous gene expression patterns, distinct somatic copy-number alterations (SCNA), as well as frequent overexpression of SPINK1 mRNA.
PTEN is a tumor suppressor gene, located on chromosome 10q23, and loss of PTEN results in upregulation of the PI3K/ AKT pathway. Loss of PTEN may occur due to homozygous deletion, nonsense mutations, promoter hypermethylation, or with loss of heterozygosity (LOH). In prostate cancer, homozygous deletions spanning the PTEN locus occurs at one of the highest rates of any tumor type studied thus far. PTEN mutations may occur in multiple exons. Approximately in 25%-70% of prostate cancer, PI3K pathway has been altered either through PI3k overactivation or PTEN inactivation. PTEN is inactivated mainly through deletion in nearly 40%, or mutations in about 10%; both are more common in advanced prostate cancer.
Activating extracellular domain ERBB2 mutations (S310F, S310Y, R157W) have been identified in urothelial carcinoma (enriched in micropapillary variant) and adenocarcinomas of breast and lung. These activating mutations may have therapeutic potential in some clinical settings.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 40-70% of Langerhans cell histiocytosis and approximately 50% of Erdheim-Chester disease. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings, and clinical trials for advanced BRAF V600 mutation-positive tumors using targeted therapy (often in combination with other therapy) may be available (clinical trials.gov).
ERBB2 exon 20 insertions occur within exon 20, which encodes part of the kinase domain. These mutations occur with a frequency of approximately 2--4% of all NSCLC. Overall, in-frame ERRB2 insertions in exon 20 have been reported in approximately 6% of cases of lung adenocarcinoma which are negative for EGFR, KRAS, ALK alterations and these variants are more frequent in patients who were never-smokers. Mutations in ERRB2 do not have an independent prognostic value in lung adenocarcinoma, according to a recent study. In vitro studies have shown that this specific variant is associated with constitutive kinase activation and is associated with sensitivity to some ERBB2 inhibitors and therefore, it may represent a targetable mutation in some clinical settings. Please refer to clinicaltrials.gov for additional information. Recommend correlation with other clinical and laboratory findings.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is mutated in a large number of cancers. It encodes a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Most PTEN mutations are loss-of-function mutations. Mono-allelic or bi-allelic loss of PTEN is found in a considerable fraction of tumors, including gliomas (75%). In glioblastoma, PTEN loss/deletion is associated with poor patient prognosis, and/or shorter disease-free survival. There are ongoing clinical trials investigating anti-tumor activity of agents in recurrent glioblastoma with this mutation.
PTEN is a tumor suppressor gene, located on chromosome 10q23. It encodes a lipid and protein phosphatase that negatively regulates the PI3K/AKT/mTOR pathway. Cancer-associated alterations in this gene often result in loss of PTEN protein and upregulation of the PI3K/AKT/mTOR pathway. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome while somatic mutations are also known to occur in multiple malignancies. PTEN p.Y68H is a reported pathogenic variant that causes tyrosine to histidine substitution at codon 68 affecting NH2-terminal phosphatase domain. This variant has been reported previously in association with PTEN-related disorders. Functional studies demonstrate that individuals harboring this variant have decreased levels of the PTEN protein when compared to wild type controls. However, its clinical significance remains to be fully elucidated.
KRAS belongs to the RAS family of oncogenes. KRAS mutations are detected in approximately 20% to 25% of lung adenocarcinoma. Contrary to most other oncogenic driver mutations, KRAS is more often found in smokers and is detected at lower frequency in East Asian patient cohorts. Mutations in KRAS are usually mutually exclusive with other oncogenic driver aberrations including EGFR, BRAF, HER2 mutations and ALK and ROS1 rearrangements. KRAS mutations in NSCLC most often occur in codons 12 or 13 and with a lower frequency in codon 61. KRAS Q22K mutation consists of a C to A transversion substituting lysine for glutamine. This KRAS variant, at codon 22, is exceedingly rare in lung cancers, and also only rarely been described in very few other cancers. Mutations at this site have also been reported as germline mutations in Noonan syndrome. The preclinical studies have shown that cell lines expressing the KRAS Q22K mutation possess high in vivo oncogenic potential, higher than that of wild-type KRAS. The prognostic as well as predictive role of this and other KRAS mutations continues to be studied. Although various attempts inhibiting KRAS have been made, there is no established therapy specific for this large patient subpopulation.
The p.T1010I mutation, in the cytoplasmic juxtamembrane domain of MET has been shown to increase growth factor independent proliferation and motility in vitro in tumor cell lines in some studies. This mutation has seen more frequently in thyroid carcinomas than in the goiter controls. But its significance has been challenged by other studies which report a low incidence of T1010I mutation in both tumors and controls and not resulting in an enhanced c-MET phosphorylation. The utility of MET pathway inhibitors also continues to be explored. This variant has also been reported as a germline variant present in less than 1% of the general population. Its role in tumor development and progression continues to be studied. Due to conflicting reports of pathogenicity, this variant best characterized as a variant of uncertain significance (VUS) (https://www.ncbi.nlm.nih.gov/clinvar/variation/41624/).
MET is frequently overexpressed in glioblastomas (GBM), and some gliomas show hepatocyte growth factor (HGF) autocrine activation of the MET signaling pathway. Several studies have found that HGF and MET are expressed at higher levels in human gliomas than in control brain tissue, and that expression levels correlate with tumor grade. Some studies have shown that the HGF expression in high-grade (WHO Grade III-IV) tumors was significantly higher than in low-grade (WHO I-II) tumors. Similarly, coexpression of HGF and MET is observed more frequently in Grade IV GBM than in low-grade glioma, consistent with the contribution of an HGF/MET autocrine loop to malignant progression in these tumors. However, MET sequence alterations have been rare. The p.T1010I mutation, in the cytoplasmic juxtamembrane domain of MET has been reported in some tumor types and also has been reported as a germline variant present in less than 1% of the general population. Its role in tumor development and progression continues to be studied. The utility of MET pathway inhibitors also continues to be explored.
This mutation, namely a 1795GTT insertion, results in BRAF V599Ins. Kinase assays on BRAF V599Ins and BRAF V600E show increased enzymatic activity, increased phosphorylation of MEK, MAPK and RSK and a high transformation rate in the cells compared to wild type BRAF. Thus, BRAF V599Ins, similar to BRAF V600E, is a 'gain of function' mutation, with constitutive activation, which accounts for its role in papillary cancer of the thyroid.
FGFR3 is one of 4 high affinity tyrosine kinase receptors for the fibroblast growth factor family of ligands. On ligand stimulation, FGFR3 undergoes dimerization and tyrosine autophosphorylation, resulting in cell proliferation or differentiation, depending on the cell context, through the mitogen-activated protein kinase (MAPK) and phospholipase Cγ signal transduction pathways. All known mutations are believed to result in ligand-independent activation of the receptor. Germ line mutations in this gene lead to craniosynostosis and multiple types of skeletal dysplasia. However, somatic mutations of FGFR3 gene are very rare in brain tumors. In some cases, the possibility of FGFR3 variants being germline can not be excluded. Clinical correlation is recommended.
RAS mutations (HRAS, NRAS and KRAS) are found in all epithelial thyroid malignancies. The frequency of KRAS mutations in thyroid carcinomas is 2-3%. Overall, RAS mutations are identified in 10--20% of papillary carcinomas (follicular variant), 40--50% of follicular carcinomas and 20--40% of poorly differentiated and anaplastic carcinomas. Of note, RAS point mutations are mutually exclusive with other thyroid mutations such as BRAF, RET/PTC, or TRK rearrangements in papillary thyroid cancers. In follicular carcinomas, RAS mutations are mutually exclusive with PAX8-PPARG rearrangements. RAS mutations have also been associated with more aggressive disease and distant metastasis. The therapeutic implications of RAS mutations in thyroid cancer are unknown at this time.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Somatic mutations in this gene may be observed in colorectal cancer (CRC), stomach cancer and desmoid tumors. Although APC mutations have been reported in up to 5% of low grade gliomas and up to 13% primary glioblastomas (GBM), evidence regarding their involvement in CNS tumors is still limited. Further studies are needed to explore the clinical value of these mutations in CNS tumors.
This GNAS mutation causes constitutive activation of the G-protein complex and activates adenylate cyclase to produce cyclic-AMP (cAMP) that can activate oncogenic pathways. The frequency of GNAS mutation in non-small cell carcinoma of the lung cases is relatively low (<5%) and its significance remains to be fully elucidated.
KRAS mutations have been reported to be present in 16 to 41% of cases of low grade serous carcinoma of the ovary. The prognostic significance of KRAS mutations in ovarian tumors is uncertain; some reports suggest that patients with KRAS G12V may have shorter overall survival than patients without mutation, while other reports suggest that KRAS mutations in some low grade carcinomas of the ovary may be associated with slightly improved prognosis. In-vitro studies showed that cell lines with KRAS G12V mutation are more sensitive to selumetinib (MEK inhibitor) compared to cells with KRAS G12D. The clinical response to MEK inhibitors in patients with these tumors and mutations remains to be elucidated.
The DNAJB1-PRKACA fusion transcript is detected in 80 to 100% of fibrolamellar hepatocellular carcinomas. Detection of DNAJB1-PRKACA is thought to be a very sensitive and specific finding in support of the diagnosis of fibrolamellar carcinoma, and may contribute to tumor pathogenesis. The therapeutic targetability of this alteration remains to be elucidated.
The nuclear receptor coactivator NCOA2 was identified as a highly significant target gene on the 8q13 amplicon and is also subject to mutation in some tumors lacking gene amplification. Copy number gains or mutations in NCOA2 and other regulators of nuclear receptor function such as NCOA2 are present in primary tumors, thereby extending the potential importance of AR pathway perturbation to disease initiation. The frequency of NCOA2 alteration could be as high as 20 and 63 percent in primary and metastatic tumors respectively. The genomic and functional data suggest that NCOA2 functions as a driver oncogene in primary tumors by increasing AR signaling, which is known to play a critical role in early and late stage prostate cancer. This may be a potentially targettable pathway alteration in some settings.
The androgen receptor (AR) is a ligand-dependent nuclear transcription factor. The AR gene undergoes multiple alterations leading to increased activity in prostate cancer, including gene amplification, point mutations, and alteration in splicing leading to constitutively active variants. However, these alterations take place largely, if not exclusively, in metastatic, castration resistant prostate cancer (CRPC). It is believed that lesions in the AR gene itself do not play a role in the pathogenesis of prostate cancer, but instead emerge during treatment as a mechanism of resistance to therapies targeting the androgen axis. Even in advanced cancers that no longer respond to androgen deprivation therapy, accumulating evidence has shown that AR signaling remains active and plays a critical role in disease progression. Androgen receptor activity, as inferred by the induction of AR target genes, was significantly increased in SPOP and FOXA1 mutant tumors when compared to normal prostate or ERG-positive tumors.
P53 activates the transcription of genes involved in cell cycle arrest, DNA repair, and apoptosis. Deletion and point mutation at the TP53 locus occur in 25%-40% and 5%-40% of prostate cancer, respectively. Although the frequency of p53 mutations seems to be lower in prostate cancer than in other cancers, these alterations are not exclusively late events, as they have been shown in 25% to 30% of clinically localized prostate cancer. Several studies indicate that p53 overexpression may be associated with poor prognosis, especially when present in combination with Bcl2. Interestingly, SPOP mutations are also mutually exclusive with deletions and mutations in the TP53 tumor suppressor.
Approximately half of all prostate cancers harbor recurrent gene fusions involving ETS transcription factors. The most common gene rearrangement is the fusion of the 5' untranslated region of TMPRSS2 (an androgen-regulated gene) and ERG (a member of ETS transcription factor family). TMPRSS2:ERG fusion is cancer-specific and results in ERG protein overexpression. ERG fusion is associated with adverse clinicopathologic predictors, metastases, and disease-specific death in non-PSA screened populations. In a cohort of active surveillance patients, it is correlated with increased tumor volume and higher Gleason grade. The effect of ERG fusions on aggressive features or outcome following radical prostatectomy is less clear and needs further elucidation.
EGFR has been reported to show increased expression in a subset of bladder cancers and may be a targetable alteration in some clinical settings.
Mutations in the Androgen Receptor are rare in untreated prostate cancer and have been described in 15-33% of castration resistant prostate cancer and hormone refractory tumors. Among these, the H875Y and T878A are recurrent mutations that have been previously described. These mutations alter responses to androgen receptor antagonists. Cases with two such mutations have been previously reported and the mutations may co-exist on the same allele.
IRS1 and IRS2 are the key protein effectors for transmitting insulin signals from the insulin-like growth factor receptor to the nucleus via the PI3K / AKT / mTOR pathway. IRS2 has been previously noted to be recurrently focally amplified in several anecdotal studies across multiple cancer types (colorectal cancer PMID: 23594372, cholangiocarcinoma PMID:26684807, glioblastoma PMID: 14655756, rhabdomyosarcoma PMID: 23578105), suggesting that this could be a "driver" alteration in a subset of cancer.. IRS2 amplifications have also been associated with sensitivity to the insulin receptor inhibitor BMS-754807 in colorectal cancer cell lines (PMID: 25527633). There is no direct evidence to connect IRS2 amplification status with sensitivity to any targeted therapy regimen in patients; however, an attractive hypothesis is that tumors harboring IRS2 amplifications could be sensitive to drugs targeting insulin signaling, PI3K, AKT, and mTOR. Drug sensitivity and exome sequencing data from colorectal patient derived tumor xenografts have associated IRS2 copy gains with sensitivity to anti-EGFR therapies (PMID: 26416732).
Smad4 is tumor suppressor gene and is crucial for thyroid development and function. It is key component of the transforming growth factor beta (TGFB) pathway which regulates the expression of thyroid-specific genes. The role of SMAD4 in thyroid tumorigenesis remains unclear. However, mutations affecting the coding region of the SMAD4 gene have been detected in some sporadic thyroid neoplasms. Studies that analyzed expression of SMAD4 in thyroid tumors gave contradictory results. Some studies showed that the expression of SMAD4 was reduced in thyroid cancer cells. Other studies indicated that it was expressed and present in the nucleus in all thyroid cell lines and controls analyzed, indicating propagation of TGFB signaling in thyroid tumors. Of note, a SMAD4 mutation C324Y, recently isolated from nodal metastases of papillary thyroid carcinoma (PTC), was confirmed to cause an increase in TGFB signaling and lead to the acquisition of transformed phenotype and invasive behavior in thyroid cells, enabling them to proliferate independently from thyroid-stimulating hormone.
FGFR3 is one of 4 high affinity tyrosine kinase receptors for the fibroblast growth factor family of ligands. On ligand stimulation, FGFR3 undergoes dimerization and tyrosine autophosphorylation, resulting in cell proliferation or differentiation, depending on the cell context, through the mitogen-activated protein kinase (MAPK) and phospholipase Cγ signal transduction pathways. Some FGFR3 mutations are believed to result in ligand-independent activation of the receptor. Somatic mutations of FGFR3 gene are not reported in thymic tumors. However, in some cases, the possibility of FGFR3 variants being germline can not be excluded. Clinical correlation is recommended.
CDKN2A gene functions as an important tumour suppressor in various human malignancies including colorectal cancer, and its activation prevents carcinogenesis via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Somatic mutations of CDKN2A are present in various tumor types but have not been well characterized in colorectal cancer. However, epigenetic silencing of CDKN2A by hypermethylation has been reported be a possible predictive factor of poor prognosis in patients with colorectal cancer.
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. KRAS mutations are frequent in low-grade mucinous tumors of appendiceal origin and pseudomyxoma peritonei (43-100%) where mutations commonly occur in codon 12 or 13, with G12D and G12V being the most common. However, appendiceal adenocarcinoma cases with goblet cell features usually lack KRAS mutations. Mutations in the KRAS gene may indicate poor prognosis and drug response with therapies targeted to EGFR in some settings. However, this should be interpreted in conjunction with other laboratory and clinical findings.
Somatic mutations in TP53 are frequent in human cancer. Germline TP53 mutations cause of Li-Fraumeni syndrome, which is associated with a range of early-onset cancers. The types and positions of TP53 mutations are diverse. TP53 mutations may be potential prognostic and predictive markers in some tumor types, as well as targets for pharmacological intervention in some clinical settings. The IARC TP53 Database (http://www-p53.iarc.fr/) is a useful resource which catalogues TP53 mutations found in cancer.
Although PDGFRA activating mutations in patients with GIST, primarily D842V, were reported to be associated with resistance to the tyrosine kinase inhibitor, Imatinib; however, PDGFRA mutations in breast cancer are very rare. Moreover, this specific missense mutation in the extracellular domain of PDGFRA, has not been reported and its clinical significance is unknown.
NKX2-1 is a lineage-specific transcription factor that is frequently focally amplified in lung adenocarcinoma (PMID 17982442). NKX2-1 amplification supports a diagnosis of lung adenocarcinoma, as this event occurs rarely in other tumor types, including in lung squamous or small-cell lung cancer. NKX2-1 has been proposed to be an oncogenic "survival factor" for lung adenocarcinomas (PMID 23763999) though studies have also demonstrated tumor suppressor effects for this gene (PMID 21471965). There is no known relationship between NKX2-1 amplification and drug sensitivity.
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. The frequency of the KRAS gene mutations in intraductal papillary mucinous neoplasms (IPMNs) varies from 38.2% to 100%. There appears to be no significant difference among the incidence of KRAS mutation in the various grades of dysplasia: 87% in low-grade, 90.2% in intermediate grade and 70.7% in high-grade dysplasia. This mutation is considered to be an early event in the neoplastic transformation of IPMNs. KRAS mutations have the highest frequency in the pancreatobiliary subtype (100%) and the lowest frequency in the intestinal subtype (46.2%). Studies demonstrate that KRAS mutations in different tumors may have various biological, prognostic, and possibly therapeutic implications in some settings.
The receptor tyrosine kinase FGFR2 is one of four fibroblast growth factor receptors designated FGFR1-4 that activate FGF signalling upon trans-autophosphorylation of the receptor dimers. Some genetic alterations of FGFR2 lead to aberrant activation of FGFR2 signaling cascades due to the creation of autocrine signaling loop or the release of FGFR2 from autoinhibition. It is known that some FGFR2 gene variations including intronic polymorphisms confer a risk for breast cancer, preferentially for estrogen receptor-positive breast tumors. FGFR2 and FGF10, the main ligand of FGFR2, are both overexpressed in 5-10% of breast tumors. Somatic missense mutations have also been reported in breast cancer leading to ligand independent activation of FGFR2. In cell line and xenograft experiments, inhibition/knockdown of FGFR2 results in anti-tumour effects, suggesting the oncogenic role of FGFR2, raising the potential of FGFR2 as a target of therapy in FGFR2 driven cancers. The P253R variant in FGFR2 has also been described in some constitutional disorders including craniosynostosis syndromes (eg, Apert syndrome).
KRAS is a gene that encodes one of the several proteins in the growth factor signaling pathway(s) and is important in the development and progression of a variety of cancers. KRAS can harbor oncogenic mutations that yield a constitutively active protein. The frequency of the KRAS gene mutations in urothelial carcinoma of urinary bladder is very low (3% to 7%), and these mutations occur in all stages and grades. In the context of bladder tumors, mutations in the KRAS gene do not appear to be predictors for recurrence-free, progression-free and disease-specific survival according to some studies.
FGFR3 is one of 4 high affinity tyrosine kinase receptors for the fibroblast growth factor family of ligands. On ligand stimulation, FGFR3 undergoes dimerization and tyrosine autophosphorylation, resulting in cell proliferation or differentiation, , through the mitogen-activated protein kinase (MAPK) and phospholipase Cg signal transduction pathways. Some FGFR3 mutations are believed to result in ligand-independent activation of the receptor. However, FGFR3 F384L mutation is not associated with activation of FGFR and, in NIH-3T3 cells, it was demonstrated to be devoid of any transforming activity. In some cases, the possibility of FGFR3 variants being of germline origin, cannot be excluded. The FGFR3 F384L mutation has been reported as a benign/likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/134404/). Clinical correlation is recommended.
The SEPT14 gene has been described as a fusion partner with EGFR in up to 4% of glioblastomas. In that context, glioma cell lines harboring this gene fusion were found to be susceptible to EGFR inhibitors in vitro. The functional significance of an isolated partial amplification of this gene would be of uncertain significance. Detection of rearrangement of this locus with a fusion partner such as EGFR would require an alternative methodology such as RNAseq or FISH analysis.
The CDKN2A gene locus is altered in up to approximately 57% of glioblastoma, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2B locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials.
The CDKN2B gene locus is altered in up to approximately 55% of glioblastoma, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2A locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials.
Amplification of FGFR1 has been reported in approximately 10% of breast cancer and may be associated with adverse outcome according to some reports. It has been reported to be associated with increased expression of FGFR1 and increased activity of downstream growth signaling pathways. Some reports suggest FGFR1 may have a role in regulating response to endocrine therapy. FGFR1 amplification may be a targetable alteration in some clinical settings (PubMed IDs: 20179196, 25400686).
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Eighty percent of all thyroid cancers are papillary thyroid carcinomas (PTCs). Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC and other well-differentiated thyroid neoplasms or nodular goiters. The K601E mutation results in an amino acid substitution at position 601 in BRAF, occurring within the highly conserved motif of the kinase domain. This is the second most common BRAF mutation found in thyroid nodules after V600E. Unlike BRAF V600E, K601E is strongly associated with follicular-patterned cancer, particularly with the encapsulated follicular variant of PTC, and may also be found in follicular thyroid carcinomas. Overall, BRAF K601E mutant tumors may show better clinical outcomes than BRAF V600E positive tumors.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are common in a wide spectrum of brain tumors but they are not described in medulloblastomas to our knowledge. BRAF F595 mutations are pathogenic in some tumor types but their clinical significance in medulloblastomas remains to be studied. Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some BRAF mutations in select tumor types in certain settings.
PIK3CA mutations have been identified in pediatric and adult gliomas including: anaplastic oligodendrogliomas, anaplastic astrocytomas, glioblastoma multiforme, rosette forming glioneuronal tumors and medulloblastomas. Although PIK3CA mutations are reported in medulloblastoma, their role in tumorigenesis remains controversial. According to some preclinical studies, mutations in PIK3CA likely activate the AKT pathway to progress, rather than initiate, WNT-medulloblastoma. PIK3CA mutations are potentially targetable in some settings and pathway inhibitors are currently under investigation.
The PTPN11gene encodes SHP-2, a widely expressed cytoplasmic protein tyrosine phosphatase. SHP-2 is essential for activation of the RAS/MAPK signaling cascade. Most mutations are gain-of-function and result in prolonged ligand-dependent activation of the RAS/MAPK cascade. Germ-line PTPN11 mutations cause Noonan syndrome, a developmental disorder characterized by an increased risk of malignancies. Activating somatic mutations in PTPN11 have been documented in certain hematologic malignancies but they are infrequent in solid tumors. According to TCGA data base, about 2% of all the glial tumors harbor somatic mutations in PTPN11 gene but their prognostic and therapeutic significance remains to be fully elucidated. The utility of SHP2 inhibitors continues to be explored in some preclinical studies.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. APC mutations have been reported in 3-10% of prostate cancers. In some studies, a high-level of APC promoter methylation was shown to be an independent predictor of a poor prognosis in prostate cancers. However, further studies are needed to explore the clinical value of APC mutations in these tumors.
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. KRAS mutations are common in both extrahepatic (40-49%) and intrahepatic (24-27%) cholangiocarcinomas. Mutations in the KRAS gene may indicate poor prognosis and drug response with therapies targeted to EGFR in some settings. Of note, RAS mutations sensitize tumors to MEK inhibitors. However, this should be interpreted in conjunction with other laboratory and clinical findings.
CDKN2A gene functions as an important tumor suppressor in various human malignancies including cholangiocarcinomas, and its activation prevents carcinogenesis via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Somatic mutations of CDKN2A are present in various tumor types including cholangiocarcinomas where they appear to be more common in extrahepatic cholangiocarcinomas (up to 15%) than in intrahepatic ones. However, epigenetic silencing of CDKN2A by hypermethylation is more frequent, and the frequency ranges from 17% to 83% in different studies. Of note, inactivation of CDKN2A may portend poor clinical outcome according to some studies. However, correlation with other clinical and lab findings is necessary.
Beta catenin is a transcriptional co-regulator and an adapter protein for cellular adhesion; it comprises part of the Wnt signaling pathway and intracellular levels of beta-catenin are regulated by its phosphorylation, ubiquitination and proteosomal degradation. Accumulation of nuclear beta catenin can lead to a tumoral phenotype and oncogenic transformation in a variety of solid tumors. Various oncogenic mutants of beta catenin have been found in different tumor types which alter its degradation, leading to its accumulation and promoting tumor growth. CTNNB1 mutations are particularly common in colorectal carcinomas associated with hereditary non-polyposis colon cancer syndrome and wild type APC gene, and are extremely rare in sporadic colorectal cancers. These mutations consist almost entirely of transitions at codons 41 and 45, and result in stabilization of a protein that resists degradation, leading to nuclear accumulation of β-catenin. Up to 50% of primary colorectal carcinomas with CTNNB1 mutations exhibit microsatellite instability, suggesting that CTNNB1 mutations may be more common in the DNA mismatch repair pathway of tumorigenesis. Microsatellite instability is generally associated with better prognosis when compared to patients with intact mismatch repair pathways. Preclinical studies suggest that CTNNB1 mutations may confer resistance to PI3K-AKT inhibitors in colorectal cancer.
PTEN is a tumor suppressor gene, located on chromosome 10q23. It encodes a lipid and protein phosphatase that negatively regulates the PI3K/AKT/mTOR pathway. Cancer-associated alterations in this gene often result in loss of PTEN protein and upregulation of the PI3K/AKT/mTOR pathway. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome while somatic mutations are also known to occur in multiple malignancies. PTEN alterations are rare and not well characterized in parathyroid tumors. One study reported loss of heterozygosity of PTEN in 7 of 14 parathyroid carcinomas. PTEN p.G165R variant is a reported pathogenic variant that causes glycine to arginine substitution at codon 165 affecting NH2-terminal phosphatase domain. This variant has been reported previously in endometrial and CNS tumors in COSMIC data base. Functional studies demonstrate that individuals harboring this variant have decreased levels of the functional PTEN protein when compared to wild type controls. However, its clinical significance remains to be fully elucidated.
Beta catenin is a transcriptional co-regulator and an adapter protein for cellular adhesion; it comprises part of the Wnt signaling pathway and intracellular levels of beta-catenin are regulated by its phosphorylation, ubiquitination and proteosomal degradation. Accumulation of nuclear beta catenin can lead to a tumoral phenotype and oncogenic transformation in a variety of solid tumors. Various oncogenic mutants of beta catenin have been found in different tumor types which alter its degradation, leading to its accumulation and promoting tumor growth. CTNNB1 mutations in prostate cancer occur rarely, in only 2-5% of cases. Currently, the function of β-Catenin in human prostate cancer continues to be explored. In the context of prostate, β-Catenin may modulate the androgen receptor (AR) pathway. Some preclinical mouse studies have shown that increased β-Catenin levels can cooperate with PTEN loss to promote the progression of aggressive invasive prostate cancer together with squamous metaplasia. Clinical correlation is recommended.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR tyrosine kinase inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions, EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. EGFR S768I (exon 20) occurs in 1–2% of EGFR mutant lung cancers and is often coincident with other EGFR mutations. EGFR S768I is reported to be sensitive to EGFR-TKIs. EGFR G724S (exon 18) is very rare and its significance is unknown.
The epidermal growth factor receptor (EGFR) is a cell surface receptor belonging to the ErbB family tyrosine kinase receptors. EGFR is involved in cell growth control through its role in the two main intracellular pathways, the mitogen-activated protein kinase (MAPK) pathway and the phosphatidylinositol 3-kinase- (PI3K-) protein kinase B (AKT) pathway. The over-expression or mutation of EGFR may be responsible for the constitutive activation of these pathways. In the colorectal cancer, the EGFR has been found to be frequently over expressed, and may be associated with tumor stage and prognosis. In a subset of such patients, the addition of anti-EGFR monoclonal antibodies to the conventional chemotherapeutic regimens may expand response rates and increase progression-free survival. Somatic EGFR mutations are infrequent in colorectal cancers. The frequency varies from 0.34 to 3.3% in Western population, and from 12% to 22.4% in Asians. R776H is a recurrent mutation in the hinge region of the kinase domain and is known to activate EGFR in a ligand independent manner. In some cases, the possibility of R776H variant being of germline origin, cannot be excluded. The clinicopathologic correlation of EGFR mutations in colorectal cancers continues to be explored.
c-kit (CD117) is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of human tissues. Gain-of-function mutations of the c-kit gene have been identified that produce ligand-independent activation of c-kit and cell proliferation. Some of these mutations appear causative in the pathogenesis of adult mastocytosis and most gastrointestinal stromal tumors (GISTs). c-kit receptor and its ligand have been demonstrated in human colon cancer cell lines. Some studies have shown high frequency of c-Kit overexpression in stage II colon cancer patients (59.3%) with significant correlation between c-Kit overexpression and reduced disease free survival. However, other studies failed to demonstrate c-kit expression in a significant number of colorectal cancers suggesting that c-kit kinase activation is not a prominent pathogenetic feature of colorectal cancers. Role of c-Kit continues to be studied in colon cancers.
Somatic mutations in GNAS are frequently found in intraductal papillary mucinous neoplasms (IPMNs) of pancreas, and have been identified in 41% to 66% of cases. All of these mutations involved codon 201 (R201C or R201H). However, the GNAS mutation was infrequent in typical pancreatic ductal adenocarcinomas (PDAs). These mutations are lead to disruption of the intrinsic hydrolytic activity of Gsα, leading to constitutive activation. GNAS mutations seem to be an early event in IPMN development. The clinical significance of these mutations remains to be established.
The anaplastic lymphoma kinase (ALK) has emerged as a potentially relevant biomarker and therapeutic target in pediatric solid and hematologic malignancies. It is a receptor tyrosine kinase (RTK) that is known to be activated either by point mutations or by chromosomal translocations. These genetic alterations act as oncogenic drivers and promote constitutive, ligand-independent activation of this RTK. Recurrent activating point mutations are seen within kinase domain in both the hereditary and sporadic form of neuroblastoma cases (7-10%). According to some studies, the presence of an ALK aberration could be a biomarker of aggressive disease and inferior clinical outcome. Clinical trials of crizotinib in neuroblastoma are underway. The R1275Q mutation is most common variant among ALK-mutated neuroblastomas (33%), and is found in both sporadic and familial cases. The R1275 amino acid substitution lies within the activation loop and causes constitutive ligand-independent activation of this RTK. Both preclinical and clinical studies suggest that this mutation could be sensitive to ALK inhibition.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions, EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M. EGFR exon 19 in-frame insertions have been described in about 1% of EGFR-mutant lung cancers. They appear to be more common in nonsmoking women. These exon 19 insertions appear to be sensitizing mutations and have been shown to respond to TKIs in some studies.
KIT mutations occur in approximately 85% of patients with gastrointestinal stromal tumors (GIST), while Exon 9 is mutated in approximately 10 ~ 15% of all KIT-mutated GIST. Compared to patients with KIT exon 11 mutations, patients with exon 9 mutations tumors show intermediate sensitivity to imatinib. Median duration of benefit from imatinib is approximately 7~12 months compared to 23 months for patients with exon 11 mutations. Patients with exon 9 mutations are more likely to respond to second line sunitinib than patients with other KIT/PDGFRA mutations.
The receptor tyrosine kinase FGFR2 is one of four fibroblast growth factor receptors designated FGFR1-4 that activate FGF signalling upon trans-autophosphorylation of the receptor dimers. Some genetic alterations of FGFR2 lead to aberrant activation of FGFR2 signaling cascades due to the creation of autocrine signaling loop or the release of FGFR2 from autoinhibition. About 10-16% of primary endometrial cancers harbor activating mutations in FGFR2. These mutations are more frequent in cancers of endometrioid histological subtype compared with serous or clear-cell subtypes. Gain-of-function mutations in the kinase domain lead to ligand-independent activation of the receptor, whereas mutations in the extracellular ligand-binding domain increase the affinity for fibroblast growth factors (FGFs). Both types of mutations have been shown to be potentially oncogenic in endometrial cancer cell lines. In cell line and xenograft experiments, inhibition/knockdown of FGFR2 results in anti-tumour effects, suggesting the oncogenic role of FGFR2, raising the potential of FGFR2 as a target of therapy in FGFR2 driven cancers. Therefore, FGFR-pathway inhibition remains potentially promising in this patient population.
KRAS belongs to the RAS family of oncogenes. KRAS mutations are detected in approximately 10-30% of endometrial tumors, predominantly within codons 12 or 13. KRAS mutations are also identified in endometrial hyperplasias, although at a lower frequency than in carcinomas. According to some studies, the gain of the KRAS function may represent an early event in endometrioid-type tumorigenesis. It has been shown that endometrioid carcinomas with significant mucinous component are more likely to have such mutations. KRAS gene amplification and protein overexpression but not mutation may be associated with aggressive and metastatic endometrial cancer according to some studies.
PTEN is a tumor suppressor gene, located on chromosome 10q23. It encodes a lipid and protein phosphatase that negatively regulates the PI3K/AKT/mTOR pathway. Cancer-associated alterations in this gene often result in loss of PTEN protein and upregulation of the PI3K/AKT/mTOR pathway. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome while somatic mutations are also known to occur in multiple malignancies, particularly as an early event in the development of endometrial cancer. PTEN gene sequence abnormalities are highly variable in type (frameshifts, point mutations) and can occur throughout all 9 exons. Germline mutations of PTEN, found in Cowden’s syndrome, are associated with an increased risk of endometrial cancer. Somatic mutations of PTEN occur in up to 50% of complex atypical hyperplasia and type I endometrial adenocarcinomas. Clinical trials assessing the efficacy of PI3K and mTOR inhibitors in PTEN loss are being explored.
SMAD4 is tumor suppressor gene and it encodes an intracellular mediator in the transforming growth factor β (TGF β) signal transduction pathway. Somatic mutations affecting the SMAD4 gene are rare in breast neoplasms and their role in breast tumorigenesis remains unclear. However, it has been demonstrated that SMAD4 protein expression is markedly downregulated or lost in breast ductal carcinoma when compared with that in the normal breast epithelium. Loss of SMAD4 protein expression may play a role in disease progression and overall prognosis in breast cancer patients but this need to be fully elucidated.
The STK11 is a tumor suppressor gene located on chromosome 19p13.3. The encoded protein has serine-threonine kinase activity. Functionally, STK11 regulates cellular energy metabolism and cell polarity by activating AMP-activated protein kinase (AMPK) and other members of the AMPK family. Germline mutations in the STK11 gene are responsible for Peutz-Jeghers syndrome, an autosomal dominant disorder with variable clinical phenotype and increased risk of some cancers. Somatic mutations of STK11 gene are reported in several tumors including lung cancers. Studies have demonstrated STK11 inactivation is a common event and may be involved in the development of sporadic lung adenocarcinoma. Inactivation mutations of STK11 are found in 30% of lung cancer cell lines and in 15% of primary lung adenocarcinomas. Clinical relevance of these alterations and impact on disease progression and patient survival needs to be fully elucidated.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions, EGFR Exon 21 L858R mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M. EGFR exon 18 mutations account for 3.6% of all the EGFR mutations in lung adenocarcinomas. Of these, G719 mutations account for the majority of them and are sensitive to anti-EGFR inhibitors. Exon 18 deletions are rare (<0.1%) and but they are potentially responsive to anti-EGFR TKIs in some small clinical case studies. Of note, they appeared to be more sensitive to second-generation TKIs, especially afatinib and neratinib, than to first- and third-generation TKIs based on in vitro experiments.
The anaplastic lymphoma kinase (ALK) has emerged as a potentially relevant biomarker and therapeutic target in a variety of solid and hematologic malignancies. It is a receptor tyrosine kinase (RTK) that is known to be activated either by point mutations or by chromosomal translocations. These genetic alterations act as oncogenic drivers and promote constitutive, ligand-independent activation of this RTK. Approximately 3-7% of non-small cell lung cancers (NSCLC) harbor ALK fusions/rearrangements. This fusion oncogene rearrangement is transforming both in vitro and in vivo and defines a distinct clinicopathologic subset of NSCLC that are highly sensitive to therapy with ALK-targeted inhibitors. While crizotinib is highly active in patients with ALK-positive NSCLC, patients have been shown to invariably develop resistance to this drug. In approximately one-third of resistant cases, tumors can acquire a secondary mutation within the ALK tyrosine kinase domain. ALK F1174 variant is a somatic mutation in the ALK kinase domain and has been detected in neuroblastomas. It has a transforming activity in vitro and in vivo, and may cause resistance to crizotinib as well as second generation ALK inhibitors such as ceritinib.
Germ line mutations of mutations in either TSC1 or TSC2 are found in 75-90% of cases of tuberous sclerosis complex (TSC), an autosomal dominant tumor syndrome associated with variable clinical phenotype including several hamrtomas and benign tumors. In addition, somatic alterations in these genes may occur in some tumor types. TSC1 and TSC2 both are tumor suppressor genes and their inactivation occurs by a classical two-hit mechanism. TSC1 is located on chromosome 9q34 and encodes hamartin. TSC2 is located on chromosome 16p13 and encodes tuberin. Hamartin and tuberin interact with and regulate a variety of proteins. These are negative regulators of the mTOR pathway, which is important for cell proliferation and frequently found activated in tumors. Mutation or deletion of TSC1 or TSC2 is found in 9-16 % of urothelial bladder tumors and up to 3% of clear cell renal cell carcinomas. More than 50% of bladder tumors of all grades and stages show LOH for markers on chromosome 9 and the TSC1 locus at 9q34 is a common critical region of deletion. Therefore, mTOR inhibitors have been identified as potential therapies for TSC1-mutated bladder cancers in some studies. LOH for the TSC1 or TSC2 locus has been described in 22% of 86 human lung cancer specimens. However, TSC1/2 sequence alterations are infrequent in lung and other epithelial malignancies.
Copy number gain (amplification) of EGFR has been reported in up to 30% of esophageal adenocarcinomas and less than 5% of gastric adenocarcinomas. According to some studies increased EGFR protein expression may be associated with decreased survival. This alteration may have therapeutic implications in some settings.
Mutations at codon R683 of JAK2, have been previously described in B-ALL (especially Down Syndrome associated B-ALL) and represent a mutational "hotspot"; Some variants at this codon (R683) are known to be activating mutations. Cases of B-ALL with JAK2 mutations tend to also show rearrangement/overexpression of CRLF2; these are potentially targetable pathway alterations. Such cases tend to have a BCR/ABL-like transcriptional signature.
NOTCH1 mutations have also recently been reported in approximately 10% of chronic lymphocytic leukemia and are typically PEST domain mutations in that disease. In CLL, NOTCH1 mutations and tend to be exlusive of SF3B1 mutations and possibly TP53 mutations, although some studies demonstrate that NOTCH1 mutations are associated with mutations of TP53. In CLL, the presence of NOTCH1 mutations has been associated with trisomy 12 and aggressive biologic features(CD38+, ZAP70+, unmutated IgH variable region) and adverse prognosis in some settings. The potential utility of therapeutic targeting of activating NOTCH1 mutations in these diseases remains to be elucidated.
TP53 is a well known tumor suppressor gene that is mutated in wide variety of cancers. In terms of myeloid disorders, missense, nonsense, and frameshift mutations of TP53 tend to occur in the DNA binding domain and have been reported in approximately 4% of cases of AML where they tend to be associated with a poorer prognosis and an adverse cytogenetic risk profile. TP53 mutations also occur in approximately 10% of patients with myelodysplastic syndrome (MDS) and are often associated with poorer prognosis, adverse cytogenetic profile and deletion of 5q either in isolation or as part of a complex karyotype.
TP53 is a well known tumor suppressor gene that is mutated in wide variety of cancers. Among cases of acute lymphoblastic leukemia, overall TP53 mutations are reported to occur in less than 10% of cases. However, TP53 mutations have a very high prevalence (approximately 90%) among cases of ALL with low hypodiploid karyotype and in this setting are often associated with monosomy 17 and may be associated with germline TP53 mutations in a significant proportion of such cases in children.
Germ line mutations of mutations in either TSC1 or TSC2 are found in 75-90% of cases of tuberous sclerosis complex (TSC), an autosomal dominant tumor syndrome associated with variable clinical phenotype including several hamrtomas and benign tumors. In addition, somatic alterations in these genes may occur in some tumor types. TSC1 and TSC2 both are tumor suppressor genes and their inactivation occurs by a classical two-hit mechanism. TSC1 is located on chromosome 9q34 and encodes hamartin. TSC2 is located on chromosome 16p13 and encodes tuberin. Hamartin and tuberin interact with and regulate a variety of proteins. These are negative regulators of the mTOR pathway, which is important for cell proliferation and frequently found activated in tumors. Mutation or deletion of TSC1 or TSC2 is found in 9-16 % of urothelial bladder tumors and up to 3% of clear cell renal cell carcinomas. More than 50% of bladder tumors of all grades and stages show LOH for markers on chromosome 9 and the TSC1 locus at 9q34 is a common critical region of deletion. Therefore, mTOR inhibitors have been identified as potential therapies for TSC1-mutated bladder cancers in some studies. LOH for the TSC1 or TSC2 locus has been described in 22% of 86 human lung cancer specimens. However, TSC1/2 sequence alterations are infrequent in lung and other epithelial malignancies.
MLH1 is a component of the cellular DNA mismatch repair (MMR) machinery causing hereditary nonpolyposis colorectal cancer (HNPCC), and is associated with specific somatic alterations in the tumor, characterized by high microsatellite instability (MSI-H). The MLH1 V384D mutation has been associated with cancer risk in some tumor types. This variant encodes in a partially impaired protein with diminished interaction with PMS2 protein and reduced MMR activity in vitro. The MLH1 V384D variant has not been reported in thyroid tumors. However, some other MLH1 variants have been described in some thyroid tumors, but their clinical significance is yet to be determined. Of note, according to one report, MLH1 V384D variant has been reported to be associated with primary resistance to EGFR-TKIs in patients with EGFR L858R-positive lung adenocarcinoma. Clinical correlation is recommended.
CDH1 on 16q22.1 encodes E-cadherin which functions in intercellular adhesion. E-cadherin is involved in transmitting chemical signals and controlling cell maturation and movement, and acts as a tumor suppressor. A lack of functional E-cadherin impairs cell adhesion and increases the likelihood of invasion and metastasis of tumor cells. More than 100 different pathogenic germline mutations are distributed throughout the CDH1 gene including splice-site sequences and have been found to cause a familial cancer disorder called hereditary diffuse gastric cancer (HDGC). Somatic CDH1 alterations are also found in approximately 30% of all patients with gastric cancers, both diffuse and intestinal types. CDH1 mutation identification in HDGC families is clinically important to assess the risk of gastric and breast cancers in unaffected relatives. Prognostic and therapeutic implications of this alterations remain to be fully elucidated. The 50 gene panel hotspot assay can not distinguish between germline or somatic(acquired) variants. Correlation with other clinical and lab findings, including genetic counseling, may be helpful, if clinically indicated.
IDH2 is a mitochondrial enzyme involved in citrate metabolism. Mutations at Arg140 and Arg172 of IDH2 are typically heterozygous and are considered gain-of-function mutations that lead to increased levels of 2-hydroxyglutarate believed to alter epigenetic regulation in various tumors, especially in myeloid neoplasms. The Arg140 mutation of IDH2 has not been reported previously in lung tumors. However, a few other IDH2 mutations have been described in non-small cell lung cancers (NSCLC) in a very small number of patients in the literature. The prognostic impact of IDH2 mutations in NSCLC remains uncertain at this time. Mutant IDH2 may provide a potential therapeutic target in some settings. Clinical correlation is recommended.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are present in approximately 50% to 60% of cutaneous melanomas and are also present at lower frequencies in other melanoma subtypes. A point mutation, L597R, is located in the kinase domain of BRAF. A case report has shown that a metastatic melanoma with this mutation is sensitive to BRAF inhibitors. In addition, it has been suggested that BRAF L597 mutations could potentially be responsive to MEK inhibitors. Drug: Trametinib BGB659
The PTPN11gene encodes SHP-2, a widely expressed cytoplasmic protein tyrosine phosphatase. SHP-2 is essential for activation of the RAS/MAPK signaling cascade. Most mutations are gain-of-function and result in prolonged ligand-dependent activation of the RAS/MAPK cascade. Germ-line PTPN11 mutations cause Noonan syndrome, a developmental disorder characterized by an increased risk of malignancies. Activating somatic mutations in PTPN11 have been documented in certain hematologic malignancies but they are infrequent in solid tumors. About 3% of all lung cancers harbor somatic mutations in PTPN11 gene but their prognostic and therapeutic significance remains to be fully elucidated. The utility of SHP2 inhibitors continues to be explored in some preclinical studies.
KRAS belongs to the RAS family of oncogenes. KRAS mutations in codons 12 and 13 were found in 6-7% of prostatic adenocarcinomas. KRAS gene rearrangement has been reported in 3% of metastatic prostate cancer. Prognostic and predictive implications of KRAS gene alterations in prostate cancer need to be fully elucidated.
SMAD4 is a tumor suppressor gene and it encodes an intracellular mediator in the transforming growth factor β (TGF β) signal transduction pathway. The gene is inactivated in 40% of human gastric cancers by loss of heterozygosity, promoter hypermethylation, and somatic mutation. Prior sequencing studies have shown that SMAD4 is mutated in up to 8% of gastric cancers. SMAD4 p.R361H mutation occurs within the MH2 domain which is the SMAD-SMAD interaction and transcription activation domain of the protein. The loss of SMAD4, especially loss of nuclear SMAD4 expression, is involved in gastric cancer progression. Mutations at codon 361 have been previously reported in various tumor types. The exact clinical significance of this mutation in gastric cancers needs to be fully elucidated.
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. KRAS mutations are found in approximately 2-3% of esophageal cancers. In colorectal cancers, mutations in the KRAS gene may indicate poor prognosis and poor drug responses against anti-EGFR therapies. However, prognostic and predictive implications of KRAS mutations in esophageal cancers need to be fully elucidated. Results should be interpreted in conjunction with other laboratory and clinical findings.
EGFR mutations have been reported in up to 5% of gastric cancers. The prognostic and predictive implications of EGFR mutations in gastric cancer have not been fully determined. Multiple clinical trials involving EGFR small molecule inhibitors and monoclonal antibodies are present, but limited and conflicting data preclude the therapeutic significance of EGFR mutations in gastric cancer. In NSCLC, an acquired T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. Third generation TKIs (e.g. osimertinib) have been shown to be effective in lung adenocarcinomas with the EGFR T790M mutation. A germline EGFR T790M mutation results in a rare lung cancer hereditary syndrome associated with increased risk in never-smokers. The presence of a germline EGFR T790M mutation also predicts for resistance to standard TKIs. The significance of EGFR T790M in gastric cancer should be considered in a relevant clinical context. Drug Resistance: Afatinib Erlotinib Gefitinib
The cytoplasmic β-catenin protein is implicated as a cell-cell adhesion regulator coupled with cadherin and is considered as a member in the wingless/Wnt signal transduction pathway. Mutations in CTNNB1, the gene encoding β-catenin, tend to impact or even eliminate APC-dependent serine and threonine phosphorylation sites in exon 3, resulting in oncogenic stabilization of the protein. Increased protein within the nuclei serves as a transcriptional factor through binding to the Tcf/Lef family. Mutations in the β-catenin gene are uncommon in NSCLC occurring in about 1-4% of the cases. Nuclear accumulation of β-catenin was found to be associated with EGFR mutations, and β-catenin overexpression was associated with NSCLC cell line resistance to gefitinib. Wnt pathway inhibitors are in preclinical development or have entered early clinical trials. Because high β-catenin expression has been associated with good outcome rather than with poor outcome in NSCLC patients, it could potentially prove important to target specific downstream β-catenin functions rather than using agents that could directly suppress β-catenin levels through upstream targeting of the Wnt pathway.
Somatic mutations in BRAF have been found in 1--4% of all NSCLC most of which are adenocarcinomas. The G466V mutation results in an amino acid substitution within the kinase domain of BRAF. Unlike other mutant BRAF proteins, G466V shows decreased kinase activity. In preclinical studies, lung cancer cell lines with G466V mutation were sensitive to TKI dasatinib, presumably by induction of tumor cell senescence. However, therapeutic implications of BRAF inhibitors in patients with this mutation need to be fully elucidated. Drug: Trametinib
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions, EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M. EGFR L747P (c.2239_2240 TT>CC) is a rare missense compound substitution mutation in the Exon 19 and has been reported to be resistant to some EGFR inhibitors.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is commonly mutated in a large number of cancers. It negatively regulates intracellular levels of Phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Mono- and bi-allelic loss of PTEN is found in approximately 40-50% and 5% of breast cancers, respectively. It has been reported to occur in BRCA1-associated basal-like breast cancer. Germline mutations in PTEN are also responsible for Cowden disease, a rare autosomal dominant multiple-hamartoma syndrome. In one study, germline mutations of PTEN have been reported to be associated with 85% lifetime risk of breast cancer in patients with PTEN hamartoma tumor syndrome. Aberrant PTEN pathway is associated with metastases and poor prognosis in breast cancer. It also predicts poor response to trastuzumab. There are ongoing clinical trials investigating anti-tumor activity of PI3K-beta inhibitor in PTEN deficient tumors.
EGFR mutations have been reported in up to 5% of gastric cancers. The prognostic and predictive implications of EGFR mutations in gastric cancer have not been fully determined. Multiple clinical trials involving EGFR small molecule inhibitors and monoclonal antibodies are present, but limited and conflicting data preclude the therapeutic significance of EGFR mutations in gastric cancer.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is commonly mutated in a large number of cancers. It negatively regulates intracellular levels of Phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. PTEN mutations have been reported in up to 19% of gastric cancers. Germline mutations in PTEN are also responsible for Cowden disease, a rare autosomal dominant multiple-hamartoma syndrome. Patients with Cowden disease can have gastric polyps, but a possible association with gastric cancer needs further study. Inactivation of PTEN is shown to be closely associated with tumor progression and metastases. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.
ERBB2 kinase domain mutations are seen in up to 4.3% of breast cancers. In vitro analyses demonstrated that L755S confer resistance to lapatinib and could potentially emerge as an acquired mutation during therapy. Another preclinical study has shown that L755S is sensitive to irreversible TKIs neratinib and canertinib. The predictive and prognostic as well as therapeutic implications of ERBB2 mutations need further elucidation.
CDKN2A gene encodes p16 and functions as an important tumor suppressor in various human malignancies. Its activation prevents carcinogenesis via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Genetic alterations (deletion, mutation, and methylation) in p16 associated with loss of function have been reported in cell lines and primary thyroid tumors. However, predictive or prognostic significance of p16 in thyroid cancer is not clear and correlation with other clinical and lab findings is necessary. Multiple clinical trials are available for patients with CDKN2A deficient tumors.
CDKN2A generates several transcript variants including p16 and p14ARF. P16 regulates cell cycle by inhibiting CDK4 and CDK6, and thus preventing progression from G1 to S phase. P14ARF acts as a tumor suppressor by inhibiting ribosome biogenesis and initiating p53-dependent cell cycle arrest and apoptosis. Mutations and deletion of CDKN2A are reported in up to 34% of gastric cancer. In addition, EBV-positive gastric adenocarcinoma showed CDKN2A promoter hypermethylation. Gastric cancer with CDKN2A mutations has been shown to be sensitive to CDK4/6 inhibitors in vitro studies. However, predictive or prognostic significance of CDKN2A mutation in gastric cancer is not clear and correlation with other clinical and laboratory findings is necessary. Multiple clinical trials are available for patients with CDKN2A deficient tumors.
KIT mutations are seen in up to 17% of cutaneous melanomas. The V559A mutation in exon 11 occurs within the juxtamembrane domain. In vitro studies have shown that mutant KIT proteins have increased kinase activity. KIT activating mutations in exons 11 and 13 are typically sensitive to treatment with Imatinib. There are multiple clinical trials available for patients with melanomas harboring KIT alterations.
EGFR mutations have been reported in 1-3% of thyroid cancers. The prognostic and predictive significance of EGFR mutations in thyroid cancer is not clear and correlation with other clinical and laboratory findings is necessary. Clinical trials involving protein kinase inhibitor are available for patients with tumors harboring EGFR mutations.
The catalytic subunit (p110a) of phosphatidylinositol-3-kinase (PI3K) is encoded by the PIK3CA gene and acts to activate several signaling cascades, including the well-characterized AKT-mTOR pathway that promotes cell survival, proliferation, growth and motility. PIK3CA is among the most commonly mutated genes in cancer and aberrant activation of PI3K is a transforming event. Somatic mutations in PIK3CA have been found in 1--3% of NSCLC and genetic alteration in PIK3CA have been identified in 7% of lung adenocarcinomas. These mutations typically occur within specific hotspot regions. PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways. The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains), with three hotspots (E542K, E545K, and H1047R/L). PIK3CA mutations have been reported in 8-21% and 20-33% of head/neck and anal squamous cell carcinoma, respectively. PIK3CA mutations, especially ones involving the helical domain, in these types of squamous cell carcinoma are highly associated with HPV. The predictive and prognostic significance of PIK3CA mutations in squamous cell carcinoma is unclear and needs further elucidation. Clinical trials targeting PI3K/Akt/mTor pathway inhibitors are available for patients with PIK3CA mutated tumors.
RAS is a family of small GTPases and acts as an oncogene. Point mutations in codons 12 and 13 of RAS gene increases its affinity for GTP and those in codon 61 inactivate its autocatalytic GTPase function, resulting in permanent RAS activation and stimulation of its downstream targets along the MAPK and PI3K/AKT signaling pathways. HRAS mutation has been reported in up to 5% and 9% of head/neck and vulvar squamous cell carcinoma, respectively. The predictive and prognostic significance of HRAS mutations in squamous cell carcinoma is unclear and needs further elucidation.
KRAS belongs to a family of small GTPases and gain-of-function mutations in the gene yield a constitutively active protein. Such mutations are found in approximately 30% to 50% of metastatic colorectal cancers and are common in other tumor types. The most frequent KRAS mutations occur at codons 12, 13, and 61. Mutations at codons 117 and 146 are less common. Mutations at codon 14 have been detected in adenocarcinomas of the small intestine and colon as well as AML. Germline V14I mutations have been identified in patients with Noonan syndrome. In vitro studies have shown that V14I mutations lead to moderately enhanced MEK1/2 and ERK1/2 phosphorylation suggesting increased downstream signaling, but with slightly less transforming capacity than G12D mutation. Mutations in the KRAS gene may indicate poor prognosis and poor drug response to EGFR-targeted therapies. Results should be interpreted in conjunction with other laboratory and clinical findings.
The anaplastic lymphoma kinase (ALK) has emerged as a potentially relevant biomarker and therapeutic target in a variety of solid and hematologic malignancies. It is a receptor tyrosine kinase (RTK) that is known to be activated either by point mutations or by chromosomal translocations. These genetic alterations act as oncogenic drivers, promoting constitutive, ligand-independent activation of this RTK. Approximately 3-7% of non-small cell lung cancers (NSCLC) harbor ALK fusions/rearrangements. ALK fusion oncogenes are transforming both in vitro and in vivo, defining a distinct clinicopathologic subset of NSCLC that are highly sensitive to therapy with ALK-targeted inhibitors. While crizotinib (ALK/MET TKI) is highly active in patients with ALK-positive NSCLC, patients have been shown to invariably develop resistance to this drug. In approximately one-third of resistant cases, tumors can acquire a secondary mutation within the ALK tyrosine kinase domain. L1196 is present in the gatekeeper position at the bottom of the ATP-binding pocket of the protein. Gatekeeper genetic alterations seem to confer TKI resistance in oncogenic tyrosine kinases. L1196M mutant confers high-level resistance to crizotinib, but has been shown to be sensitive to ceretinib.
The anaplastic lymphoma kinase (ALK) has emerged as a potentially relevant biomarker and therapeutic target in a variety of solid and hematologic malignancies. It is a receptor tyrosine kinase (RTK) that is known to be activated either by point mutations or by chromosomal translocations. These genetic alterations act as oncogenic drivers, promoting constitutive, ligand-independent activation of this RTK. Approximately 3-7% of non-small cell lung cancers (NSCLC) harbor ALK fusions/rearrangements. ALK fusion oncogenes are transforming both in vitro and in vivo, defining a distinct clinicopathologic subset of NSCLC that are highly sensitive to therapy with ALK-targeted inhibitors. While crizotinib (ALK/MET TKI) is highly active in patients with ALK-positive NSCLC, patients have been shown to invariably develop resistance to this drug. In approximately one-third of resistant cases, tumors can acquire a secondary mutation within the ALK tyrosine kinase domain. ALK G1202R is postulated to be in the solvent-exposed region abutting the crizotinib-binding site, likely diminishing the binding affinity of crizotinib and other ALK inhibitors to the mutant ALK. G1202R has been shown to cause resistance to crizotinib as well as second generation ALK inhibitors (ceritinib, alectinib).
PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways. The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains), with three hotspots (E542K, E545K, and H1047R/L). PIK3CA mutations have been reported in various tumor types including up to 36% and 11% of hepatocellular carcinoma and gastric cancer, respectively. They are detected less frequently in cholangiocarcinoma (~6%) and pancreatic adenocarcinoma (~4%). The predictive and prognostic significance of PIK3CA mutations is unclear and needs further elucidation. Clinical trials targeting PI3K/Akt/mTor pathway inhibitors are available for patients with PIK3CA mutated tumors.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Approximately 8-15% of colorectal cancer (CRC) harbors BRAF mutations. BRAF G469A mutation in exon 11 is infrequent in CRC and occurs within the kinase domain. The presence of BRAF mutation is significantly associated with right-sided colon cancers and is associated with decreased overall survival. BRAF mutation in a microsatellite unstable colorectal carcinoma indicates that the tumor is probably sporadic and not associated with Lynch syndrome (HNPCC). However, if a BRAF mutation is not detected, the tumor may either be sporadic or Lynch syndrome associated. Detection of BRAF mutations may also be useful in determining patient eligibility for anti-EGFR treatment. Some studies have reported that patients with metastatic CRC (mCRC) that harbor BRAF mutations do not respond to anti-EGFR antibody agents (cetuximab or panitumumab) in the chemotherapy-refractory setting. Results should be interpreted in conjunction with other laboratory and clinical findings.
PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and RAS-RAF-MAPK pathways. The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains). Activating mutations in PIK3CA are found in a wide variety of human cancers including up to 4% of prostate cancers. The role of PIK3CA mutations as prognosticators of outcome or predictors of therapeutic response awaits further evaluation. Clinical trials are available for patients with PIK3CA mutated tumors.
MET is a member of the receptor tyrosine kinase and proto-oncogene playing a major role in tumor development and metastasis. MET mutations have been reported in 1% of primary prostate cancers and up to 4.4% of metastatic prostate cancers. Studies have suggested that overexpression of c-MET and aberrant activation of the HGF/c-MET axis in prostate cancer is a relatively late event in tumor progression seen in advanced stages of the disease. MET E168D mutation is located in the SEMA domain containing the ligand binding site. The prognostic and predictive significance of MET mutations in prostate cancer is not clear and correlation with other clinical and laboratory findings is necessary.
KRAS belongs to the RAS family of oncogenes and is important in the development and progression of a variety of cancers. KRAS can harbor oncogenic mutations that yield a constitutively active protein. The frequency of KRAS gene mutations in upper tract urothelial carcinoma is low (5%). In the context of urothelial carcinoma of the bladder, mutations in the KRAS gene do not appear to be predictors for recurrence-free, progression-free and disease-specific survival according to some studies. The prognostic and predictive role of KRAS mutations in upper tract urothelial carcinoma needs to be further elucidated.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is commonly mutated in a large number of cancers. It negatively regulates intracellular levels of Phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. PTEN somatic point mutations are infrequent, but allelic loss or altered expression is seen in approximately 20% and 40% of the melanoma cases, respectively. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.
CDKN2A gene functions as an important tumor suppressor via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. CDKN2A is the major high-risk susceptibility gene identified in melanoma. Somatic mutations of CDKN2A are reported in up to 19% and 20% of cutaneous and desmoplastic melanoma, respectively. Germline mutations have been reported in ~20-40% of families with melanoma. Correlation with other clinical and lab findings is necessary.
CDKN2A gene functions as an important tumor suppressor via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Somatic mutations of CDKN2A are present in various tumor types including ~2-3% of hepatocellular carcinoma (HCC). However, epigenetic silencing of CDKN2A by promoter hypermethylation is more frequent, occurring in 73% of HCC, 56% of HBV-related HCC, and 84% of HCV-related HCC. Clinical trials for CDKN2A deficient tumors are available. Correlation with other clinical and lab findings is necessary.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are present in approximately 50% to 60% of cutaneous melanomas and are also present at lower frequencies in other melanoma subtypes. A point mutation, N581S, is located in the kinase domain of BRAF. It has been reported that N581S is associated with intermediate kinase activity. Correlation with other clinical and lab findings is necessary.
MET is a member of the receptor tyrosine kinase and proto-oncogene playing a major role in tumor development and metastasis. Mutations in MET have been reported in 4-9% of cutaneous melanoma. MET E168D has not been reported in melanomas. This mutation is located in a conserved domain containing the ligand binding site. In vitro studies have shown that E168D may be associated with higher ligand affinity and higher susceptibility to c-Met inhibitors in lung cancer. The prognostic and predictive significance of MET mutations in melanoma is not clear and correlation with other clinical and laboratory findings is necessary.
The protein encoded by the RB1 gene is a negative regulator of the cell cycle and was the first tumor suppressor gene identified. The active, hypophosphorylated form of the protein binds transcription factor E2F1. RB1 alterations including mutations and deletions are seen in up to 11% of glioblastomas. It has been suggested that patients with RB1-deficient tumors do not respond to cyclin-dependent kinase (CDK) inhibitors. The predictive and prognostic significance of RB1 mutations in glioblastoma needs to be further studied.
KIT is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of human tissues. Somatic mutations of KIT are only identified in ~ 4% of thymic carcinoma, but KIT protein overexpression has been observed in up to 88% of cases. Valine at amino acid position 560 (V560) is located in exon 11 within the juxtamembrane domain of KIT, and an in-frame deletion of V560 results in an activating mutation. A case report has described a patient with thymic carcinoma harboring KIT V560del who had a partial response to imatinib. In another case, patient who has kit mutation in his thymic carcinoma achieved 27 moths of disease control with imatinib followed by sunitinib. Results should be interpreted in conjunction with other laboratory and clinical findings.
CDH1 on 16q22.1 encodes E-cadherin which functions in intercellular adhesion. E-cadherin is involved in transmitting chemical signals and controlling cell maturation and movement, and acts as a tumor suppressor. A lack of functional E-cadherin impairs cell adhesion and increases the likelihood of invasion and metastasis of tumor cells. Invasive lobular breast cancer (ILC) accounts for 10-15% of invasive breast cancers and is characterized by loss of E-cadherin expression due to mutations, loss of heterozygosity and hypermethylation. Germline CDH1 mutations have been found to cause a familial cancer disorder called hereditary diffuse gastric cancer (HDGC). CDH1 mutation identification in HDGC families has important clinical implications for gastric and breast cancers risk assessment in unaffected family members. The estimated risk for invasive lobular carcinoma in females with germline CDH1 mutations is approximately 40% by age 80 years. Prognostic and therapeutic implications of this alteration remain to be fully elucidated. The 50 gene panel hotspot assay cannot distinguish between germline or somatic (acquired) variants. Correlation with other clinical and lab findings, including genetic counseling, may be helpful, if clinically indicated.
This gene is often mutated in uveal melanoma (Van Raamsdonk, et al. 2010). A frequent mutation in GNA11 (Q209) can promote disease progression. Combined mTOR/PI3K and MEK inhibition is showing promises in preclinical studies (Khalili et al, 2012). In addition, a randomized, open-label, phase 2 clinical trial comparing selumetinib vs chemotherapy showed selumetinib resulted in a modestly improved progression-free survival and response rate; however, no improvement in overall survival was observed. Improvement in clinical outcomes was accompanied by a high rate of adverse events (Carvajal et al, 2014). Also, GNAQ and GNA11 mutations occur in 9.5% of mucosal melanoma and are associated with poor prognosis (Sheng et al, 2016).
Basal cell carcinoma (BCC) is primarily driven by the Sonic Hedgehog (Hh) pathway. Eighty-five percent of the BCCs harbors mutations in Hh pathway genes. In basal cell carcinoma, activating mutations in SMO are associated with sensitivity to Hedgehog pathway inhibitors.
Somatic mutations in PIK3CA have been found in 10-30% of colorectal cancers. KRAS, NRAS, BRAF and PIK3CA and non-functional PTEN predict resistance to anti-EGFR therapies in metastatic colorectal cancer. According to some reports, co-occurrence of both exon 9 and exon 20 PIK3CA mutations, when present, may be associated with a poor prognosis. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use may be associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation may be a molecular biomarker that predicts response to aspirin therapy. PIK3CA may also be a target of directed therapy in some clinical settings.
Some studies have demonstrated activity of sonic hedgehog pathway inhibitors in a subset of medulloblastomas harboring alterations in this pathway.
MDM2 encodes a nuclear-localized E3 ubiquitin ligase that may promote tumor formation by targeting tumor suppressor proteins, such as p53, for proteasomal degradation. Overexpression or amplification of this locus has been detected in a variety of different cancers. MDM2 copy number gain has been shown to be useful in distinguishing dedifferentiated liposarcoma from spindle and pleomorphic sarcomas . The prognostic value of MDM2 copy number gain remains to be fully elucidated. Small molecular inhibitors of the MDM2:p53 axis are currently in early phase clinical trials for a number of malignancies.
MAP2K2 mutations result in constitutive ERK phosphorylation and may be associated with higher resistance to MEK inhibitors. However these inhibitors are currently undergoing clinical trials and their efficacy and/or lack of toxicity has not yet been demonstrated.
MAP2K1 mutations result in constitutive ERK phosphorylation and may be associated with higher resistance to MEK inhibitors. However these inhibitors are currently undergoing clinical trials and their efficacy and/or lack of toxicity has not yet been demonstrated.
The p.C121S mutation has been associated with resistance to mutant BRAF inhibitors.
FGFR1 activating mutations may be associated with response to the multitargeted tyrosine kinase inhibitor pazopanib.
Although CEBPA mutations have been described in AML, the significance of this mutation in this tumor is unclear.
Although CEBPA mutations have been described in AML, the significance of this mutation in this tumor is unclear.
CDC73 mutations have been previously reported in parathyroid tumors. However, it could be a germ line alteration.
The BTK p.C481S variant has been previously reported to be associated with Ibrutinib resistance in patients with chronic lymphocytic leukemia.
Activating mutations in AKT1 may be associated with sensitivity to AKT inhibitors.
PTCH1 loss of function mutations are associated with Vismodegib sensitivity in basal cell carcinoma. However, the clinical significance in other tumor types is unknown.
The W844C mutation is associated with resistance to Vismodegib in basal cell carcinoma.
Activating somatic mutations in the tyrosine kinase domain of MET are found in about 10–15% of sporadic papillary renal cell carcinoma (pRCC). MET mutations are predominantly associated with Type 1 pRCC tumors. The responses to foretanib an oral inhibitor of MET and other tyrosine kinases including VEGFR2, have been described in patients with papillary renal cell cancer.
KRAS mutations are infrequent in gastric carcinomas and have been reported in approximately 6% of cases. Studies have shown no statistically significant difference in survival between KRAS-mutated and KRAS-non-mutated gastric carcinomas. However, one study showed a trend that the presence of a KRAS mutation was associated with better overall survival in gastric carcinoma patients. There is an increased frequency of KRAS mutations in gastric carcinomas with microsatellite instability. In gastric cancer, the predictive ability of KRAS has not been extensively studied, but a small study did not demonstrate an effect on survival in patients treated with an EGFR inhibitor.
In AML, presence of exon 17 mutations in KIT may confer an adverse prognosis or increased relapse rate. However, its significance in brain tumors is yet to be determined.
In AML, presence of exon 17 mutations in KIT may confer an adverse prognosis or increased relapse rate. However, its significance in renal cancer is yet to be determined.
This gene is often mutated in uveal melanoma. A frequent mutation in GNAS/QNA11 (Q209) can promote disease progression. Combined mTOR/PI3K and MEK inhibition is showing promises in preclinical studies.
FGFR3 mutations may be associated with response to the multi-targeted tyrosine kinase inhibitor pazopanib.
FGFR2 mutation in a patient with oral squamous cell carcinoma was associated with response to the multitargeted tyrosine kinase inhibitor pazopanib. The clinical significance of this finding in this tumor type is unknown.
FGFR2 mutation in a patient with oral squamous cell carcinoma was associated with response to the multitargeted tyrosine kinase inhibitor pazopanib.
Although FGFR2 mutation in a patient with oral squamous cell carcinoma was reported to be associated with response to the multitargeted tyrosine kinase inhibitor pazopanib, FGFR2 mutations in bladder cancer are very rare. The clinical significance of this finding is unknown.
FGFR1 amplification is associated with poor survival in patients with resected squamous cell lung cancer. FGRF1 amplification may be associated with sensitivity to the multitargeted tyrosine kinase inhibitor pazopanib.
FGFR1 amplification may be associated with sensitivity to the multitargeted tyrosine kinase inhibitor pazopanib in some tumor types.
The FGFR1 copy number gain is part of a large partial chrom 8 gain. The role of FGFR1 in prostate cancer is under study. FGRF1 amplification may be associated with sensitivity to pazopanib in some tumor types.
Melanomas with ERBB4 mutations may be associated with sensitivity to Lapatinib.
In colorectal cancer, EGFR gene amplification is associated with sensitivity EGFR-targeted therapies, such as Erbitux and Vectibix.
The CDKN2B gene locus is altered in up to approximately 60% of bladder cancer, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2A locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials.
CDC73 mutations have been previously reported in parathyroid tumors.
Some mutations in BRCA2 may be associated with sensitivity to PARP inhibitors. The effect of this missense mutation is not entirely clear. Drug: Rucaparib Niraparib Olaparib
Inactivating mutations in BRCA1 may be associated with sensitivity to PARP inhibitors. Drug Rucaparib Niraparib Olaparib
The ALK gene encodes a receptor tyrosine kinase that is recurrently altered by chromosomal rearrangements in multiple malignancies, and the prevalence of oncogenic ALK fusions in lung adenocarcinoma is approximately 5%. The EML4-ALK fusion is known to be oncogenic. Crizotinib is a tyrosine kinase inhibitor that is FDA approved for treatment of ALK-fusion positive lung non-small lung carcinoma.
AKT3 is closely related to AKT1. Activating mutations in AKT1 such as p.E17K may be associated with sensitivity to AKT inhibitors. AKT3 activating mutations might also confer sensitivity to AKT inhibitors, although the significance of this variant is uncertain.
AKT2 is closely related to AKT1. Activating mutations in AKT1 such as p.E17K may be associated with sensitivity to AKT inhibitors. AKT2 activating mutations might also confer sensitivity to AKT inhibitors, although the significance of this variant is uncertain.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are present in approximately 50% to 60% of cutaneous melanomas and are also present at lower frequencies in other melanoma subtypes. A point mutation, D594G, is located in the kinase domain of BRAF. Mutations at residue D594 are believed to result in an impaired kinase activity. Correlation with other clinical and lab findings is necessary.
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. Such mutations are found in approximately 30% to 50% of metastatic colorectal tumors and are common in other tumor types. KRAS L19F has been previously reported in colorectal cancers, but its oncogenic and transforming potential was reported to be significantly lower compared to codons 12 or 13 KRAS mutants. The predictive and prognostic significance of this specific mutation in KRAS needs further elucidation. Results should be interpreted in conjunction with other laboratory and clinical findings.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Pancreatic cancer is considered a low risk cancer, though it is observed in FAP families with higher incidence than the general populations. Somatic APC mutations have been reported in ~1% of pancreatic ductal adenocarcinomas (PDAC). Codon I1307 lies within a regulatory region of the APC protein mediated by ubiquitination. APC I1307K is associated with increased colorectal cancer risk by making the gene unstable and prone to acquire mutations during normal cell division. The germline APC I1307K gene mutation is most commonly found in people of Ashkenazi Jewish descent. Therefore, routine colorectal screening is very important in these individuals. The prognostic and therapeutic implications of APC mutations in PDAC remain to be fully elucidated. Correlation with other clinical and lab findings is recommended.
IDH-mutant tumors have aberrant production and accumulation of the oncometabolite 2-hydroxyglutarate (2-HG), which may play a pivotal oncogenic role in several malignancies including AML, central nervous system and biliary tract. Strikingly, IDH1 mutations were rarely detected in the other solid tumor types. IDH1 mutation has been reported in up to 2% of colorectal adenocarcinomas. The clinical significance of this mutation with regards to response to anti-IDH1 therapy in colorectal cancer is unknown. Results should be interpreted in conjunction with other laboratory and clinical findings.
EGFR mutations have been reported in up to 21% of glioblastoma tumors (GBM). In GBM, EGFR mutations typically cluster in the extracellular domain and include in-frame deletions and missense mutations. However, mutations (such as V774M) in the tyrosine kinase domain of EGFR have been previously reported in GBM. The clinical significance of this mutation with regards to response to TKI therapy in GBM needs further elucidation. Results should be interpreted in conjunction with other laboratory and clinical findings.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Somatic mutations in this gene may be observed in colorectal cancer (CRC), stomach cancer and desmoid tumors. Although APC mutations have been reported in ~2% of ovarian serous adenocarcinomas, further studies are needed to explore the clinical value of these mutations in ovarian cancers. Results should be interpreted in conjunction with other laboratory and clinical findings.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are infrequent in small intestinal adenocarcinoma, ranging from 1% to13% of reported cases. BRAF N581S mutation is located in the kinase domain and has been associated with intermediate kinase activity. Mutations in the kinase region of BRAF have been associated with resistance to anti-EGFR therapy in colorectal cancers. The prognostic and predictive significance of this specific BRAF mutation in small intestinal adenocarcinoma needs further elucidation. Results should be interpreted in conjunction with other laboratory and clinical findings.
In breast cancer, ERBB2 (HER2) amplification and over-expression are associated with sensitivity to anti-HER2 agents, such as Trastuzumab. Drug : Lapatinib + Trastuzumab, Pertuzumab + Trastuzumab, Ado-trastuzumab emtansine, Lapatinib, Trastuzumab,
CDK (cyclin-dependent kinase) 4 and CDK6 are key players in cell cycle progression. In many human cancers, CDK6 is overactive, for example one third of medulloblastoma patients show upregulated CDK6. In 2015, FDA has granted an approval to CDK4/6 inhibitor palbociclib (Ibrance) as a frontline treatment for postmenopausal women with ER-positive, HER2-negative metastatic breast cancer. However, per NCCN 2016 guideline for breast cancer, this treatment regime does not require the amplification of CDK4/6. Palbociclib, along with other CDK inhibitors, are actively under many other clinical trials targeting liposarcoma, various advanced solid tumors and hematologic malignancies.
CDK (cyclin-dependent kinase) 4 and CDK6 are key players in cell cycle progression. In many human cancers, CDK4 is overactive, such as liposarcoma. In 2015, FDA has granted an approval to CDK4/6 inhibitor palbociclib (Ibrance) as a frontline treatment for postmenopausal women with ER-positive, HER2-negative metastatic breast cancer. However, per NCCN 2016 guideline for breast cancer, this treatment regime does not require the amplification of CDK4/6. Palbociclib, along with other CDK inhibitors, are actively under many clinical trials targeting liposarcoma, various advanced solid tumors and hematologic malignancies.
Aurora A is a member of a family of mitotic serine/threonine kinases, playing an important role in cell proliferation. AURKA amplification may be associated with sensitivity to Aurora Kinase inhibitors. However these inhibitors are currently undergoing clinical trials and their efficacy and/or lack of toxicity has not yet been demonstrated.
In lung adenocarcinomas, CRKL amplification may be associated with resistance to EGFR-directed therapy (Cheung et al, 2011). However, its significance in urothelial cancer is yet to be determined.
CRKL (Crk-like protein) is a substrate of the BCR-ABL tyrosine kinase, and plays a role in fibroblast transformation by BCR-ABL. It is potentially oncogenic. In lung adenocarcinomas, CRKL amplification may be associated with resistance to anti-EGFR therapy.
This gene encodes a member of the epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases. Amplification of ERBB3 and/or overexpression of its protein have been reported in numerous cancers, including prostate, bladder, non small cell lung cancer, endometrial cancer and breast tumors. Several ERBB3 inhibitors are under various clinical trials against different types of solid tumors, including non small cell lung cancer, breast cancer, ovarian cancer and gastric cancer.
The protein of CCND1 (Cyclin D 1) belongs to the highly conserved cyclin family, functioning as regulators of CDK kinases. This cyclin forms a complex with and functions as a regulatory subunit of CDK4 or CDK6, whose activity is required for cell cycle G1/S transition. This protein has been shown to interact with tumor suppressor protein Rb and the expression of this gene is regulated positively by Rb. Amplification of this gene, which alters cell cycle progression, are observed frequently in a variety of tumors. Cyclin D1 and the mechanisms it regulates have the potential to be a therapeutic target for cancer drugs, including inhibition of Cyclin D1, induction of Cyclin D1 degradation, and inhibition of Cyclin D1/CDK 4/6 complex.
Activation of FGFR protein family can lead to the activation of RAS-MAPK and PI3K-AKT pathways. Amplification of FGFR2 has been observed in lung adenocarcinoma, lung squamous cell carcinoma, endometrial carcinoma, urothelial carcinoma, germ cell tumor and breast cancers. Anti-FGFR2 agents are actively under multiple clinical trials against many types of solid tumor, including lung squamous cell carcinoma, gastric cancer, endometrial cancer, and cholangiocarcinoma. Germeline mutations in FGFR2 are also associated with multiple craniosynostosis syndromes.
KIT, also known as proto-oncogene c-Kit or tyrosine-protein kinase Kit or CD117, is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of tissue types. Signaling through CD117 plays a role in cell survival, proliferation, and differentiation. Altered forms of this receptor may be associated with some types of cancers. Somatic mutations of KIT in lung adenocarcinoma are relatively rare, reported up to 3.3% of the cases. The predictive and prognostic significance of KIT mutations in lung adenocarcinomas needs further elucidation. Results should be interpreted in conjunction with other laboratory and clinical findings.
KIT, also known as proto-oncogene c-Kit or tyrosine-protein kinase Kit or CD117, is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of tissue types. Signaling through CD117 plays a role in cell survival, proliferation, and differentiation. Altered forms of this receptor may be associated with some types of cancers. Somatic mutations of KIT in esophageal cancers are relatively rare, observed in up to 3.3% of the cases. The predictive and prognostic significance of KIT mutations in esophageal cancers needs further elucidation. Results should be interpreted in conjunction with other laboratory and clinical findings.
SMAD4 is a tumor suppressor gene encoding an intracellular mediator in the transforming growth factor β (TGF β) signal transduction pathway. SMAD4 mutations have been observed in ~3% of cervical cancers. Functional inactivation of SMAD4 was found in 4 of 13 cervical squamous cancer cell lines, mostly due to homozygous loss. Loss of protein expression did not correlate with loss of heterozygosity and mutations in cervical squamous carcinomas; however, it was associated with poor disease-free and overall 5-year survival in one study. The predictive and prognostic significance of SMAD4 mutations in cervical cancers needs further elucidation. Results should be interpreted in conjunction with other laboratory and clinical findings.
SMAD4 is a tumor suppressor gene encoding an intracellular mediator in the transforming growth factor β (TGF β) signal transduction pathway. SMAD4 mutations have been reported in up to 2% of urothelial carcinomas. The predictive and prognostic significance of SMAD4 mutations in urothelial carcinoma needs further elucidation. Results should be interpreted in conjunction with other laboratory and clinical findings.
IDH1 is an enzyme localized to the cytoplasm and peroxisomes and involved in citrate metabolism. IDH-mutant tumors have aberrant production and accumulation of the oncometabolite 2-hydroxyglutarate (2-HG), which may play a pivotal oncogenic role in several malignancies including AML, central nervous system and biliary tract. Strikingly, IDH1 mutations were rarely detected in the other solid tumor types. IDH1 mutations have been reported in 1-2% of lung adenocarcinomas. The clinical significance of this mutation with regards to response to anti-IDH1 therapy in lung cancer is unknown. Results should be interpreted in conjunction with other laboratory and clinical findings.
ERBB2 encodes a member of the epidermal growth factor (EGF) receptor family of receptor tyrosine kinases. ERBB2 mutations have been reported in ~2-3% of lung adenocarcinomas. The majority of ERBB2 mutations are in-frame insertions in exon 20, which encodes part of the kinase domain; however, point mutations (L755S and G776C) have also been identified. Lung adenocarcinomas with ERBB2 mutations are mutually exclusive with EGFR, KRAS, ALK alterations and these variants are more frequent in patients who are never-smokers. Mutations in ERRB2 do not have an independent prognostic value in lung adenocarcinoma, according to a recent study. In vitro analyses have shown that ERBB2 L755P and L755S mutations are associated with constitutive kinase activation and resistance to lapatinib treatment. The predictive significance of ERBB2 mutations in lung adenocarcinomas needs further elucidation. Recommend correlation with other clinical and laboratory findings.
Amplification of MET, the hepatocyte growth factor receptor, is identified in 7% of Esophagus-Stomach cancer in recent TCGA study. Several studies investigated the relationship between MET amplification and expression with the clinical outcome in patients with gastric cancer, but yielded conflicting results. Multiple clinical trials of using anti-MET agent in the treatment of Esophagus-Stomach cancer are available.
This mutation is located at extracellular domain. Patients with mutation of ERBB2 S310F, which is very close to S295 and also an extracellular domain, have been treated successfully with anti-HER agents (Jia et al, 2014; Vornicova et al, 2014). Although mutation at extracellular domain does not elevate HER2 protein level (negative for IHC), it might still activate HER2 protein or it’s downstream signaling.
PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and RAS-RAF-MAPK pathways. The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains). Activating mutations in PIK3CA are found in a wide variety of human cancers including up to 5% of renal cell carcinomas. The role of PIK3CA mutations as prognosticators of outcome or predictors of therapeutic response awaits further evaluation. Clinical trials are available for patients with PIK3CA mutated tumors.
CDKN2A gene encodes p16 and functions as an important tumor suppressor in various human malignancies. Its activation prevents carcinogenesis via induction of cell growth arrest and senescence. The majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6, leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Genetic alterations in CDKN2A have been reported in up to 41% of pancreatic adenocarcinomas (36% CNV loss and 5% SNV alterations). Few studies have suggested that CDKN2A is a causative gene in familial pancreatic cancer families. Germline mutations of CDKN2A among patients with pancreatic cancer are rare (<1%), with estimated penetrance of 58% and 39% for pancreatic cancer and melanoma, respectively. Multiple clinical trials are available for patients with CDKN2A deficient tumors. Predictive and prognostic significance of CDKN2A alterations in pancreatic cancer is not clear and correlation with other clinical and lab findings is necessary.
This mutation is recognized as gain of function mutation. Tumor with this mutation responds to neratinib, a type of TKI which is against HER2 and EGFR.
An acquired HER2 gatekeeper mutation induces resistance to neratinib in a patient with HER2 mutant-driven breast cancer
The FOXL2 gene resides on chromosome band 3q22.3 and encodes forkhead box protein L2, a forkhead-winged helix family transcription factor that is expressed in the eyelid and gonad during embryogenesis and actively maintains ovarian follicles during adulthood. A somatic missense mutation in FOXL2 (p.C134W; c.402C>G) is identified in 97% of adult granulosa cell tumor, and absent in other ovarian cancers. The prognosis and target treatment in regard of FOXL2 mutation is unknown.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are present in approximately 50% to 60% of cutaneous melanomas and are also present at lower frequencies in other melanoma subtypes. Mutations at protein residue G464 are rare in melanoma and have not been reported in previous sequencing studies. The G464V mutation results in an amino acid substitution within the highly conserved motif of the kinase domain. This specific mutation is a low frequency cancer-associated variant classified as an intermediate activity mutant that moderately increases ERK activation and can transform cells. The predictive significance of this mutation needs further study. Clinical correlation is recommended.
Somatic mutations in BRAF have been found in up to 10% of all NSCLC, more common in adenocarcinomas. D594 is a highly conserved residue within the kinase domain of BRAF and mutation of this residue appears to result in kinase inactivation. In vitro study has shown that kinase-dead BRAF forms a constitutive complex with CRAF in the presence of activated RAS leading to MEK and ERK signaling. The predictive and prognostic significance of this mutation needs further study. Clinical correlation is recommended.
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. Such mutations are found in approximately 30% to 50% of metastatic colorectal tumors and are common in other tumor types. Mutations in the KRAS gene may indicate poor prognosis and poor drug response with therapies targeted to EGFR. The absence of a KRAS mutation predicts a greater likelihood of response to EGFR-targeted therapies and improved survival with such treatment. The relevant KRAS mutation is in one of five codons (12 13, 61, 117 or 146). The presence of KRAS mutations in codon 12, 13 or 61 is associated with a high likelihood of resistance to therapies targeting EGFR. However, preclinical studies have shown that G13D mutant cell lines have intermediate sensitivity to cetuximab and panitumumab. Results should be interpreted in conjunction with other laboratory and clinical findings.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR tyrosine kinase inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions, EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. EGFR S768I (exon 20) occurs in 1–2% of EGFR mutant lung cancers and is often coincident with other EGFR mutations. S768I and V769L have previously been identified in the same NSCLC tumors. There are conflicting data regarding the sensitivity to EGFR-TKIs of tumors harboring S768I and V769L mutations. Correlation with other clinical and laboratory findings is necessary.
GNAS is a component of the heterotrimeric G-protein complex that has been shown to be mutated in 3-7% of colorectal cancers. Mutations at codon R201 of GNAS are typically activating mutations which have been described in various types of solid tumors. These mutations result in disruption of the intrinsic hydrolytic activity of Gsa, leading to constitutive activation. The clinical significance of these mutations in colorectal cancer remains to be established. Correlation with other clinical and laboratory findings is recommended.
MET is a member of the receptor tyrosine kinase and proto-oncogene playing a major role in tumor development and metastasis. MET mutations have been reported in ~2% of colon cancers. MET E168D mutation is located in a conserved domain containing the ligand binding site. In vitro studies have shown that E168D may be associated with higher ligand affinity and higher susceptibility to c-Met inhibitors in lung cancer. The prognostic and predictive significance of MET mutations in colon cancer is not clear and correlation with other clinical and laboratory findings is necessary.
CDKN2A gene functions as an important tumor suppressor via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. CDKN2A is a major high-risk susceptibility gene identified in melanoma. Somatic mutations of CDKN2A are reported in up to 19% and 20% of cutaneous and desmoplastic melanomas, respectively. Germline mutations have been reported in ~20-40% of families with melanoma. CDKN2A V126D mutation has been reported in numerous cases of familial melanoma and shown to be a loss-of-function mutation with reduced CDK4 binding. Correlation with other clinical and lab findings is necessary.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are infrequent in small intestinal adenocarcinoma, ranging from 1% to 13% of reported cases. D594 is a highly conserved residue within the kinase domain of BRAF and mutation of this residue appears to result in kinase inactivation. In vitro study has shown that kinase-dead BRAF forms a constitutive complex with CRAF in the presence of activated RAS leading to MEK and ERK signaling. The predictive and prognostic significance of this specific BRAF mutation in small intestinal adenocarcinoma needs further study. Results should be interpreted in conjunction with other laboratory and clinical findings.
MET is a member of the receptor tyrosine kinase and proto-oncogene playing a major role in tumor development and metastasis. MET mutations have been reported in up to 3.3% of low-grade gliomas and 2.2% of glioblastomas. MET E168D mutation is located in a conserved domain containing the ligand binding site. In vitro studies have shown that E168D may be associated with higher ligand affinity and higher susceptibility to c-Met inhibitors in lung cancer. The predictive and prognostic significance of MET mutations in brain tumors is unclear and needs to be further studied. Correlation with other clinical and laboratory findings is recommended.
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. KRAS mutations have been reported in up to 1.6% of low-grade gliomas and in 1% of glioblastomas. KRAS mutations have not previously reported in ganglioglioma. The predictive and prognostic significance of KRAS mutations in ganglioglioma is unclear and needs to be further studied. Correlation with other clinical and laboratory findings is recommended.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated as the mutation cluster region (MCR) and result in a truncated protein product. Somatic APC mutations are rare in adenocarcinoma of small intestine and further studies are needed to explore the clinical value of these mutations. Results should be interpreted in conjunction with other laboratory and clinical findings.
EGFR mutations in GBM cluster in the extracellular (EC) domain and include in-frame deletions (such as the common “variant III” del 6-273) and missense mutations (A289V, A289D, T263P, G598V). Mutations involving residue R108 have been reported in GBM, frequently occurring with other EGFR mutations at amino acids A289, P596, and G598. In vitro studies have shown that R108K mutation leads to increased ligand-binding affinity and shows anchorage-independent growth and tumorigenic potential when stably expressed in NIH-3T3 cells. The predictive and prognostic significance of this mutation at R108 needs further elucidation. Correlation with other clinical and laboratory findings is recommended.
The V654A c-KIT kinase domain mutation has been associated with imatinib-resistant GIST relapse, representing about 47% of all GIST secondary mutations. GIST harboring KIT V654A is still sensitive to Sunitinib and Sorafenib. drug: Nilotinib, Sunitinib
NRAS is a member of the RAS family of oncogenes. Activating point mutations in NRAS gene have been reported in a wide variety of tumors and they mostly concentrate in codons 12, 13 and codon 61. Activating mutations in NRAS are rare in pancreatic ductal adenocarcinomas (PDAC). The predictive and prognostic significance of NRAS mutations in PDAC is unclear and needs to be further studied. Correlation with other clinical and laboratory findings is recommended.
IDH2 R172X mutations have been detected in 55-82% of sinonasal undifferentiated carcinomas (SNUC). These tumors may be amenable to IDH2-targeted therapies.
PDGFRA amplification is reportedly present in up to 29% of pediatric and 21% of adult high-grade astrocytomas when assessed by fluorescent in situ hydridization. Copy number alterations of this gene have been reported in approximately 11% of adult glioblastoma making it the second most commonly altered receptor tyrosine kinase after EGFR. In those adult glioblastomas that are IDH-mutant, there is evidence to suggest that amplification of PDGFRA is associated with worse overall survival.
Mutations in beta catenin (CTNNB1) are seen in about 90% of adamantinomatous craniopharyngiomas and mutations in BRAF (V600E) in papillary craniopharyngiomas. Adamantinomatous and papillary craniopharyngiomas have been shown to carry clonal mutations that are typically mutually exclusive but may occasionally coexist. These findings indicate that the adamantinomatous and papillary subtypes have distinct molecular underpinnings, each principally driven by mutations in a single well-established oncogene - CTNNB1 in the adamantinomatous form and BRAF in the papillary form, independent of age. This may have implications for the diagnosis and treatment of these tumors. Treatment with the BRAF inhibitor vemurafenib has been reported to result in disease stabilization in a patient with a papillary craniopharyngioma with a BRAF V600E mutation.
AKT1 mutations have been reported in a variety of tumor types such as endometrial, lung, breast, colorectal, ovarian, urothelial and prostate cancers. The mutations are mutually exclusive from PIK3CA mutations. Increased expression and activation of AKT1 observed in many cancers is caused by a variety of different mechanisms including genomic alterations of AKT1, PIK3CA, PTEN, RAS family members, or growth factor receptors. Gain-of-function alterations of AKT1 can lead to neoplastic transformation in model systems, and is a potential target for therapeutic strategies. The E17K variant is by far the most frequent AKT1 mutation reported, implicating it as an important tumor promoting event.
Erlotinib Afatinib Gefitinib
This gene is a known cancer gene. ARID1A/BAF250A subunit of the SWI/SNF (BAF) chromatin remodeling complex has emerged as recurrently mutated in a broad array of tumor types and a potential tumor suppressor. There is evidence indicating that ARID1A-mutated cancers may be subjected to therapeutic intervention.
Somatic mutations in TP53 are frequent in human cancer. Germline TP53 mutations cause of Li-Fraumeni syndrome, which is associated with a range of early-onset cancers. The types and positions of TP53 mutations are diverse. TP53 mutations may be potential prognostic and predictive markers in some tumor types, as well as targets for pharmacological intervention in some clinical settings. The IARC TP53 Database (http://www-p53.iarc.fr/) is a useful resource which catalogues TP53 mutations found in cancer.
NTRK1, NTRK2, and NTRK3 alterations, including gene fusion events, have been described in a subset of infiltrating gliomas including pediatric high grade infiltrating astrocytomas within the cerebral hemispheres as well as diffuse midline gliomas.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF V600E lies within the activation segment of the kinase domain of the BRAF protein and confers a gain of function. BRAF mutations are infrequent in urothelial carcinoma and are identified in 3-5% of cases. Various BRAF inhibitors (Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings. The use of BRAF inhibitors in a number of other cancer types harboring BRAF V600E mutations are under investigation (clinicaltrials.gov). The clinicopathologic effects of BRAF in urothelial carcinoma remains to be fully elucidated.
FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. Codons 465 and 505 are some of the most frequently mutated sites in the FBXW7 gene. FBXW7 is mutated in approximately 15% of small bowel cancers. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin; however, the clinical utility remains unknown.
Beta catenin is a transcriptional co-regulator and an adapter protein for cellular adhesion; it comprises part of the Wnt signaling pathway and intracellular levels of beta-catenin are regulated by its phosphorylation, ubiquitination and proteosomal degradation. Accumulation of nuclear beta catenin can lead to a tumoral phenotype and oncogenic transformation in a variety of solid tumors. Various oncogenic mutants of beta catenin have been found in different tumor types which alter its degradation, leading to its accumulation and promoting tumor growth. Alterations in genes coding for members of the APC/b (beta)-catenin pathway have been identified in 20--25% of acinar cell carcinomas. These included inactivating mutations in APC as well as activating mutations in CTNNB1. CTNNB1 alterations have been identified in approximately 9% of pancreatic acinar cell carcinomas. CTNNB1 G34E is a rare mutation and does not lie within any known functional domains of the CTNNB1 protein. One study has shown that this mutation results in resistance to degradation, leading to increased pathway activation. Preclinical studies in CTNNB1 mutated solid tumors are underway. The full clinicopathological significance of CTNNB1 G34E remains to be further elucidated in pancreatic acinar cell carcinoma.
ERBB2 encodes HER2, an EGFR receptor tyrosine kinase, which activates PI3K-AKT-mTOR and RAS-RAF-MEK-ERK pathways. ERBB2 (HER2) amplification has been implicated in several tumor types. ERBB2 (HER2) G776V lies within the protein kinase domain of the ERBB2 protein. G776V has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on ERBB2 protein function is unknown. ERBB2 kinase domain mutations are seen in up to 4.3% of breast cancers. In a preclinical study, AP32788 (EGFR and ERBB2 TKI) inhibited growth of transformed cell lines over expressing ERBB2 G776V in culture. The clinicopathologic significance of this variant remains to be further elucidated.
The epidermal growth factor receptor (EGFR) is a cell surface receptor belonging to the ErbB family tyrosine kinase receptors. EGFR is involved in cell growth control through its role in the two main intracellular pathways, the mitogen-activated protein kinase (MAPK) pathway and the phosphatidylinositol 3-kinase- (PI3K-) protein kinase B (AKT) pathway. The over-expression or mutation of EGFR may be responsible for the constitutive activation of these pathways. In colorectal cancer, EGFR has been found to be frequently over expressed, and may be associated with tumor stage and prognosis. Somatic EGFR mutations are infrequent in colorectal cancers. The frequency of EGFR mutations in colorectal cancer varies from 0.34 to 3.3% in Western population, and from 12% to 22.4% in Asians. In a subset of patients with EGFR mutations in colorectal cancer, the addition of anti-EGFR monoclonal antibodies to the conventional chemotherapeutic regimens may expand response rates and increase progression-free survival. EGFR V765M lies within the protein kinase domain of the protein. In lung cancer, the V765M has been reported as a sensitizing mutation to EGFR tyrosine kinase inhibitors. The correlation of EGFR gene mutations with clinicopathologic characteristics in colorectal cancers continues to be explored.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions, EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M. EGFR K757M has been reported as a rare variant lung adenocarcinoma, but the significance remains to be elucidated.
EGFR (HER1), epidermal growth factor receptor, is a tyrosine kinase receptor, which activates RAS/RAF/MEK and PI3K/AKT/mTOR pathways, leading to increased cell proliferation and growth. EGFR G721S lies within the protein kinase domain of the EGFR protein. G721S has been identified in the scientific literature in lung cancer, but has not been biochemically characterized and therefore, its effect on EGFR protein function is unknown. EGFR mutations are rare and in prostate adenocarcinoma and are identified in only about 1% of cases. The clinicopathologic significance of the EGFR G721S variant in prostate cancer remains to be fully elucidated.
CDKN2A gene functions as an important tumor suppressor via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of RB and p53 pathways. CDKN2A alterations have been reported as frequent mutations in squamous cell carcinomas of different primary sites including the lung, head and neck, and skin. CDKN2A R80* results in a premature truncation and confers a loss of function to the CDKN2A protein as demonstrated by loss of CDK binding. CDKN2A truncating mutations, including R80*, have been described in approximately 4% of esophageal squamous cell carcinomas. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials. The clinical significance of the loss of one copy of CDKN2A remains to be fully elucidated in squamous cell carcinoma of the esophagus. These results should be interpreted in the clinicopathologic context.
CDKN2A gene functions as an important tumor suppressor via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of RB and p53 pathways. CDKN2A alterations have been reported as frequent mutations in squamous cell carcinomas of different primary sites including the lung, head and neck, and skin. CDKN2A R58* results in a premature truncation and confers a loss of function to the CDKN2A protein as demonstrated by loss of CDK binding. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials. The clinical significance of the loss of one copy of CDKN2A remains to be fully elucidated in squamous cell carcinoma of the bladder. These results should be interpreted in the clinicopathologic context.
CDKN2A H83Y lies within the ANK3 domain of the CDKN2A protein. H83Y confers a loss of function to the CDKN2A protein as demonstrated by loss of cell cycle control. The CDKN2A gene locus is altered in up to approximately 57% of glioblastoma, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2B locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials. CDKN2A mutations account for only 1-3% of glioblastomas and the clinical significance remains to be elucidated.
CDKN2A gene encodes p16 and functions as an important tumor suppressor in various human malignancies. Its activation prevents carcinogenesis via induction of cell growth arrest and senescence. The majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. CDKN2A alterations are common, occurring in 60-70% of gallbladder carcinomas, by mechanisms including point mutations, chromosomal loss, and promoter methylation. These somatic CDKN2A alterations are associated with a poor prognosis. A frameshift insertion at codon 57 in exon 2 will result in early truncation of the p16 protein. Multiple clinical trials are available for patients with CDKN2A deficient tumors.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. BRAF mutations are present in approximately 50% to 60% of cutaneous melanomas and are also present at lower frequencies in other melanoma subtypes. The G469R variant accounts for less than 1% of mutations overall in melanoma; however, it has been shown to account for 13% of non-V600E BRAF mutations in a study of advanced melanoma cases. The G469R mutation results in an amino acid substitution at position 469 in BRAF and occurs within the highly conserved motif of the kinase domain. Amino acid substitutions at this positon have been shown to retain variable levels of kinase activity compared to the normal BRAF. The effect of this mutation (p.G469R) on the kinase activity of BRAF is unknown. Correlation with other clinical and lab findings is recommended.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated as the mutation cluster region (MCR) and result in a truncated protein product. A study of APC gene mutations in gastric carcinomas did not find an obvious relationship between the APC mutation and tumor size, depth of invasion, node metastasis or clinical stages, indicating a limited role of the APC mutation in predicting prognosis of gastric carcinomas. APC mutations were significantly more frequent in intestinal type gastric cancers as compared with diffuse type gastric cancers, suggesting that APC gene is not only a predisposing gene in colorectal cancer but also a predisposing gene in intestinal type of gastric cancer.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Codon I1307 lies within a regulatory region of the APC protein mediated by ubiquitination. Germline APC I1307K is associated with increased colorectal cancer risk by making the gene unstable and prone to acquire mutations during normal cell division. The germline APC I1307K gene mutation is most commonly found in people of Ashkenazi Jewish descent. Therefore, routine colorectal screening is very important in these individuals. APC somatic mutations are found in less than 1% of thyroid carcinomas. The I1307K has not been reported as a somatic mutation in thyroid carcinoma to date. The prognostic and therapeutic implications of somatic APC mutations in thyroid carcinoma remain to be fully elucidated. Correlation with other clinical and lab findings is recommended.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. There is a case report of renal cell carcinoma occurring in a patient with attenuated FAP and a heterozygous germline APC deletion. Somatic APC mutations have been reported in ~1% of clear cell renal cell carcinomas. Codon I1307 lies within a regulatory region of the APC protein mediated by ubiquitination. APC I1307K is associated with increased colorectal cancer risk by making the gene unstable and prone to acquire mutations during normal cell division. The germline APC I1307K gene mutation is most commonly found in people of Ashkenazi Jewish descent. Therefore, routine colorectal screening is very important in these individuals. The prognostic and therapeutic implications of APC mutations in renal cell carcinoma remain to be fully elucidated. Correlation with other clinical and lab findings is recommended.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Somatic mutations in APC have been reported in around 2% of breast carcinomas. One study found that APC mutations in up to 18% of their breast cancer cohort and at a significantly high frequency in advanced stages of primary breast cancers. The APC K1454E variant has not been previously reported in breast carcinoma. The significance of this variant should be interpreted within the clinical context.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Approximately 10% of cutaneous squamous cell carcinomas harbor somatic mutations in BRAF. The G469A mutation in exon 11 results in an amino acid substitution at position 469 in BRAF, which occurs in the highly conserved motif of the kinase domain. Most mutant BRAF proteins, such as G469A, have increased kinase activity and are transforming in vitro. Though BRAF mutations and targeted therapies have been have been studied in other solid tumors, the predicative and prognostic significant in cutaneous squamous cell carcinoma is unclear and needs to be further investigated.
FBXW7 is a tumor suppressor gene that is mutated in several tumors including colorectal, liver, bladders and ovarian cancers. It is also mutated in endometrial and head and neck squamous cancers. FBXW7 mutations are rare in pancreatic adenocarcinoma and are present in less than 1% of tumors. Preclinical data suggest that FBXW7 mutations may sensitize cells to mTOR inhibitors. The full pathologic significance of FBXW7 mutations in pancreatic adenocarcinoma remains to be more fully elucidated.
NOTCH1 is a transmembrane receptor, which plays a role in cell fate determination, growth, and survival. Somatic activating mutations are common in T-cell lymphoblastic leukemia/lymphoma. Somatic alterations in NOTCH1 are very rare in colorectal adenocarcinoma and are identified in less than 1% of cases. NOTCH1 L2457V does not lie within any known functional domains of the NOTCH1 protein. L2457V has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on protein function is unknown. The L2457V variant has been reported as a benign/likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/380420/). These results should be interpreted in the clinicopathologic context.
Nilotinib Dasatinib Sorafenib Imatinib
Somatic APC mutations are common events in colorectal adenocarcinomas, reported in up to 76% of the cases. Loss of normal APC function is known to be an early event in both familial and sporadic colon cancer pathogenesis, occurring at the pre-adenoma stage. APC mutations do not appear to significantly affect the prognosis of colorectal cancer patients. While there are a number of small molecule inhibitors in development that target the Wnt pathway, there is currently no matched targeted therapy available for colorectal cancer patients harboring an APC mutation. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Codon I1307 lies within a regulatory region of the APC protein mediated by ubiquitination. APC I1307K is associated with increased colorectal cancer risk by making the gene unstable and prone to acquire mutations during normal cell division. The germline APC I1307K gene mutation is most commonly found in people of Ashkenazi Jewish descent. Therefore, routine colorectal screening is very important in these individuals. Correlation with other clinical and lab findings is recommended.
FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. FBXW7 R505C lies within the WD4 repeat region and confers a loss of FBXW7-substrate interaction and impairs substrate degradation by FBXW7, resulting in sustained NICD and MYC expression. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin; A single study has reported only limited activity in phase I trials using mTOR inhibitors in patients with advanced cancers including colorectal cancer. The clinical utility remains unknown.
SMAD4 is tumor suppressor gene and it encodes an intracellular mediator in the transforming growth factor b (TGF b) signal transduction pathway. Somatic mutations in SMAD4 are exceedingly rare in glial neoplasms. SMAD4 I525V has been reported as a likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/41788/). These results should be interpreted in the clinical context.
NRAS gene belongs to the family of RAS genes. It encodes a G protein that is important in the transmission of growth-promoting signals from the cell surface receptors to the nucleus through RAS-RAF-mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)-AKT cell signaling pathways. NRAS mutations are rare in glial neoplasms and are found in about 1% of cases. The clinicopathologic significance of NRAS mutations in glial neoplasms remains to be further elucidated.
MET is frequently overexpressed in glioblastomas (GBM), and some gliomas show hepatocyte growth factor (HGF) autocrine activation of the MET signaling pathway. Several studies have found that HGF and MET are expressed at higher levels in human gliomas than in control brain tissue, and that expression levels correlate with tumor grade. Some studies have shown that the HGF expression in high-grade (WHO Grade III--IV) tumors was significantly higher than in low-grade (WHO I--II) tumors. Similarly, coexpression of HGF and MET is observed more frequently in Grade IV GBM than in low-grade glioma, consistent with the contribution of an HGF/MET autocrine loop to malignant progression in these tumors. However, MET sequence alterations have been rare. The MET M362T variant is classified as a benign/likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/93565/). These results should be interpreted in the clinical context.
The CDKN2A gene locus is altered in up to approximately 57% of glioblastoma, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2B locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. W110* results in early truncation and confers a loss of function as demonstrated by loss of CDK binding and cell cycle control in culture. The clinicopathologic effects of the heterozygous rather than homozygous loss of CDKN2A in glial neoplasms remains to be further elucidated. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Somatic APC mutations have been reported in less than 1% of breast invasive ductal carcinoma. Codon I1307 lies within a regulatory region of the APC protein mediated by ubiquitination. Germline APC I1307K is associated with increased colorectal cancer risk by making the gene unstable and prone to acquire mutations during normal cell division. The germline APC I1307K gene mutation is most commonly found in people of Ashkenazi Jewish descent. Therefore, routine colorectal screening is very important in these individuals. The prognostic and therapeutic implications of APC mutations in breast carcinoma remain to be fully elucidated. Correlation with other clinical and lab findings is recommended
NOTCH1 is a transmembrane receptor, which plays a role in cell fate determination, growth, and survival. Somatic activating mutations are common in T-cell lymphoblastic leukemia/lymphoma. Somatic alterations in NOTCH1 are very rare in breast invasive ductal carcinoma and are identified in less than 1% of cases. NOTCH1 L2457V does not lie within any known functional domains of the NOTCH1 protein. L2457V has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on protein function is unknown. The L2457V variant has been reported as a benign/likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/380420/). These results should be interpreted in the clinicopathologic context.
FGFR1 is a receptor tyrosine kinase activated upon binding of the FGF ligand, which activates RAS-MAPK and PI3K-AKT pathways. Altered function of FGFR1 in cancer may lead to increased cell proliferation and decreased apoptosis. The most common alteration of FGFR1 in lung adenocarcinoma is amplification and point mutations are rare (1% of cases). FGFR1 T141R does not lie within any known functional domains of the FGFR1 protein. T141R has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on protein function is unknown. T141R has been reported as a somatic mutation in one case of lung adenocarcinoma in the literature. The clinicopathologic significance of FGFR1 T141R remains to be further elucidated.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). BRAF mutation frequencies are highly controversial in biliary tract cancers ranging from 0 to 33% for BRAF V600E. As most studies with high BRAF mutation rates were performed on European cohorts, this has raised the question of whether these discordant results represent a regional difference in the genetics of biliary tract cancer. In large cohort of biliary tract cancers including intrahepatic cholangiocarcinomas, extrahepatic cholangiocarcinomas, and adenocarcinomas of the gallbladder, BRAF V600E mutations were only rarely found in intrahepatic cholangiocarcinomas and were not identified in any cases of gallbladder adenocarcinoma. The clinicopathologic significance of BRAF V600E remains to be further elucidated in adenocarcinoma of the gallbladder. Various BRAF inhibitors (Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings. These results should be interpreted in the clinical and radiographic context.
FBXW7 is a tumor suppressor gene that is mutated in several tumors including colorectal, liver, bladder and ovarian cancers. It is also mutated in endometrial, esophageal, and head and neck squamous cancers. FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. FBXW7 R505G lies within the WD repeat 4 of the FBXW7 protein. R505G has been identified in the scientific literature, but has not been biochemically characterized and therefore, its effect on FBXW7 protein function is unknown. Preclinical data suggest that FBXW7 mutations may sensitize cells to mTOR inhibitors, however, the response to mTOR inhibitors and the clinicopathologic effects of FBXW7 R505G remains to be further elucidated.
Proto-oncogene tyrosine-protein kinase receptor RET, activates the MAPK pathway for cell proliferation and the PI3K/AKT pathway for cell survival. RET activating mutations and rearrangements are common in medullary thyroid carcinomas. 25-30% of medullary thyroid carcinomas are associated with germline RET mutations. In these germline mutations, the most commonly affected codons are 609, 611, 618, 620 (exon 10) and 634 (exon 11), encoding for the extracellular cysteine-rich domain, and codons 768 (exon 13) and 804 (exon 14) of the intracellular tyrosine kinase domain. Sporadic RET mutations have been reported in 61.5% of medullary thyroid carcinomas. In sporadic cases, the M918T mutation is most commonly reported and may indicate a poor prognosis. Given these identified molecular alterations, therapies targeting the RET signaling pathway have been used and shown to provide advantages over traditional cytotoxic therapy with regard to disease response. There are multiple ongoing clinical trials on cabozantinib (tyrosine kinase inhibitor), sorafenib (multikinase inhibitor), and everolimus (mTOR inhibitor).
Proto-oncogene tyrosine-protein kinase receptor RET, activates the MAPK pathway for cell proliferation and the PI3K/AKT pathway for cell survival. Certain inherited mutations in the RET proto-oncogene predispose individuals to the multiple endocrine neoplasia type 2 (MEN 2) cancer syndromes including MEN 2A and 2B, and familial medullary thyroid carcinoma. Somatic mutations in RET are rare in squamous cell carcinoma of the lung and are found in 2-3% of cases. RET E623K lies within the extracellular domain of the RET protein, but has not been characterized and therefore its effect on RET protein function is unknown. RET E623K has been reported as a benign germline mutation in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/24906/). These results should be interpreted in the clinical context.
Afatinib Erlotinib Gefitinib
Afatinib Erlotinib Gefitinib
Sensitive to: Afatinib Erlotinib Gefitinib
Afatinib Erlotinib Gefitinib AP32788
Drug: Trametinib BGB659
Afatinib Erlotinib Gefitinib
Drug: Trametinib
DRUG: Trametinib
Trametinib
Vemurafenib Dabrafenib Dabrafenib + Trametinib Vemurafenib + Cobimetinib
Imatinib
Dasatinib Nilotinib
Imatinib
Vemurafenib Dabrafenib Dabrafenib + Trametinib
Vemurafenib
Drug Vemurafenib Dabrafenib Dabrafenib + Trametinib Vemurafenib + Cobimetinib
Regorafenib Sunitinib Imatinib
Vemurafenib
Vemurafenib Dabrafenib Dabrafenib + Trametinib
DRUG: Trametinib
Regorafenib Sunitinib Imatinib
Imatinib
Sunitinib
Nilotinib Sorafenib Imatinib
Nilotinib Dasatinib Sunitinib Imatinib
Imatinib
Imatinib
Imatinib
Regorafenib
Imatinib
Imatinib
Sunitinib
Sunitinib Imatinib Nilotinib
Imatinib
Imatinib
Sorafenib
Imatinib
Sunitinib
Sunitinib Imatinib
Nilotinib Dasatinib Sorafenib Regorafenib Sunitinib
Sunitinib
Regorafenib Sunitinib Imatinib
Imatinib Nilotinib Dasatinib Sorafenib
FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. Due to the disruption of the WD repeat domain, the FBXW7 R393* truncating mutation is predicted to lead to a loss of FBXW7 protein function. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin; however, the clinical utility remains unknown. A single study has reported only limited activity in phase I trials using mTOR inhibitors in patient with advanced cancers including colorectal cancer.
RAS/RAF path mutation has been identified in 5-9 % of CLL patients. The K601E mutation results in an amino acid substitution at position 601 in BRAF, occurs within the highly conserved motif of the kinase domain. Most mutant BRAF proteins, such as K601E, have increased kinase activity and are transforming in vitro. Preclinical studies suggest that downstream signaling induced by the K601E mutant may be blocked by the BRAF inhibitor, vemurafenib.
Crizotinib
Imatinib
Sorafenib
Imatinib
Imatinib Dasatinib
Imatinib
Imatinib Nilotinib
Imatinib
Sunitinib Imatinib
Vemurafenib Dabrafenib Dabrafenib + Trametinib Vemurafenib + Cobimetinib Trametinib
Drug: Trametinib
Vemurafenib Dabrafenib Dabrafenib + Trametinib Vemurafenib + Cobimetinib Vemurafenib + Panitumumab Encorafenib + Binimetinib + Cetuximab Radiation + Trametinib + Fluorouracil
Trametinib
Sunitinib
Imatinib
Afatinib Erlotinib Gefitinib
Somatic mutations in BRAF have been found in 1-4% of all NSCLC most of which are adenocarcinomas. The G466R mutation results in an amino acid substitution within the kinase domain of BRAF. Unlike other mutant BRAF proteins, G466R shows decreased kinase activity, however, it also causes paradoxically activation Erk signaling in cell culture Therapeutic implications of BRAF inhibitors in patients with this mutation need to be fully elucidated.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Approximately 8--15% of colorectal cancer (CRC) harbors BRAF mutations. BRAF G469V mutation in exon 11 is infrequent in CRC and occurs within the kinase domain. The presence of BRAF mutation is significantly associated with right-sided colon cancers and is associated with decreased overall survival. BRAF mutation in a microsatellite unstable colorectal carcinoma indicates that the tumor is probably sporadic and not associated with Lynch syndrome (HNPCC). However, if a BRAF mutation is not detected, the tumor may either be sporadic or Lynch syndrome associated. Detection of BRAF mutations may also be useful in determining patient eligibility for anti-EGFR treatment. Some studies have reported that patients with metastatic CRC (mCRC) that harbor BRAF mutations do not respond to anti-EGFR antibody agents (cetuximab or panitumumab) in the chemotherapy-refractory setting. Results should be interpreted in conjunction with other laboratory and clinical findings.
MLH1 is a component of the cellular DNA mismatch repair (MMR) machinery. The MLH1 V384D mutation has been associated with cancer risk in some tumor types. This variant encodes in a partially impaired protein with diminished interaction with PMS2 protein and reduced MMR activity in vitro. The MLH1 V384D variant has not been reported as a somatic mutation in glial brain tumors. This variant has an allele frequency of 4% in the East Asian population. Some studies have shown that patients carrying the MLH V384D variant have an increased risk of the development of microsatellite-instable as well as -stable colorectal cancer. MLH1 V384D variant has also been reported to be associated with primary resistance to EGFR-TKIs in patients with EGFR L858R-positive lung adenocarcinoma. Of note, this variant is reported as a benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/41632/). Clinical correlation is recommended.
KRAS is a gene that encodes one of the several proteins in the epidermal growth factor receptor (EGFR) signaling pathway that is important in the development and progression of cancer. KRAS can harbor oncogenic mutations that yield a constitutively active protein. Such mutations are found in approximately 30% to 60% of small intestine adenocarcinomas and are common in other tumor types. The relevant KRAS mutation is in one of five codons (12 13, 61, 117 or 146). KRAS mutations in small intestine tumors are associated with higher pT classification and more frequent pancreatic invasion. The effect of KRAS mutations on drug therapy has not been well established in the literature, however it has been extensively studied in colorectal adenocarcinoma. Mutations in the KRAS gene may indicate poor prognosis and poor drug response with therapies targeted to EGFR in colon cancer, and the absence of a KRAS mutation predicts a greater likelihood of response to EGFR-targeted therapies and improved survival with such treatment. The presence of KRAS mutations in codon 12, 13 or 61 is associated with a high likelihood of resistance to therapies targeting EGFR in colon cancer. In addition, mutations at codons 117 and 146 may also be associated with reduced response to EGFR-targeted therapies in colon cancer. Results should be interpreted in conjunction with other laboratory and clinical findings.
BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and is frequently mutated in papillary thyroid carcinoma (PTC). The BRAF V600E-like PTC's (BVL) and the RAS-like PTC (RL-PTC) are fundamentally different in their genomic, epigenomic, and proteomic profiles. The BRAF V600E mutation in Exon 15 is the most common BRAF mutation has been reported in 45% of patients with PTC. BRAF F468S is a rare somatic variant in Exon 11 and is located in the tyrosine kinase domain of the BRAF protein. The clinicopathologic effects of this variant as a somatic mutation in cancer has not been established in the literature. However, a mutation at the same location, F468C, has been shown to be a gain of function mutation. This variant has also been previously reported as a pathogenic germline variant in ClinVar associated with Cardio-facio-cutaneous syndrome. These results should be interpreted in the clinical context.
KDR encodes the protein VEGF2, a receptor tyrosine kinase that regulates angiogenesis and vascular development. While KDR mutations are rare, amplification or protein overexpression have been reported in small proportion of a variety of solid tumors. KDR P263T has not been characterized and the effect on protein function is unknown. These results should be interpreted in the clinical context.
Colorectal cancers (CRCs) frequently harbor somatic mutations in the pathway members SMAD4. The prevalence of SMAD4, SMAD2, and SMAD3 mutations in sporadic CRCs was 8.6% (64 of 744), 3.4% (25 of 744), and 4.3% (32 of 744), respectively. SMAD4 R361C lies at a hotspot residue within MH2 domain and has displayed reduced SMAD4 transactivating activity in cell assays. Somatic SMAD4 mutations have been reported to be more common in advanced stages of CRCs. Studies of loss of function somatic mutations and studies of loss of heterozygosity (LOH) at the SMAD4 locus have shown an association with poor prognosis. SMAD4 mutations were also associated with mucinous histology. There are ongoing clinical trials for colorectal tumors harboring SMAD4 alterations.
Balversa (erdafitinib) has been FDA approved for treatment of urothelial carcinoma with susceptible FGFR3 or FGFR2 genetic alterations. FGFR3 is a receptor tyrosine kinase in the RAS-MAPK and PI3K-AKT pathways. FGFR3 has been found to be mutated in up to 64% of cases of bladder cancer and 40% of upper urothelial tract (ureter and renal pelvis) urothelial carcinomas. FGFR3 mutations tend to be exclusive of RAS mutations ,TP53 overexpression, TP53 mutation, but not PIK3CA mutations. However, subsets of cases with co-mutations have been described. Gain of function FGFR3 mutations (including FGFR3 R248C and FGFR3 S249C) are believed to lead to constitutive activation of the receptor and activation of the RAS-MAPK pathway. FGFR3 mutations are often seen in non-muscle invasive bladder cancers and tend to correlate with low stage and grade; however, FGFR3 mutations have also been described in muscle-invasive bladder cancer.
The STK11 is a tumor suppressor gene located on chromosome 19p13.3. The encoded protein has serine--threonine kinase activity. Functionally, STK11 regulates cellular energy metabolism and cell polarity by activating AMP-activated protein kinase (AMPK) and other members of the AMPK family. Germline mutations in the STK11 gene are responsible for Peutz--Jeghers syndrome, an autosomal dominant disorder with variable clinical phenotype and increased risk of some cancers. Somatic mutations of STK11 gene are reported in several tumors including lung cancers. Studies have demonstrated STK11 inactivation is a common event and may be involved in the development of sporadic lung adenocarcinoma. Inactivation mutations of STK11 are found in 15% of primary lung adenocarcinomas and 33% of large cell neuroendocrine carcinomas of the lung. Clinical relevance of these alterations and impact on disease progression and patient survival needs to be fully elucidated.
PDGFRA amplification is reportedly present in up to 29% of pediatric and 21% of adult high-grade astrocytomas when assessed by flourescent in situ hydridization. Copy number alterations of this gene have been reported in approximately 11% of adult glioblastoma making it the second most commonly altered receptor tyrosine kinase after EGFR. In those adult glioblastomas that are IDH-mutant, there is evidence to suggest that amplification of PDGFRA is associated with worse overall survival. Somatic mutations within the PDGFRA gene are less frequent than amplifications. PGDFRA N659K is within the tyrosine kinase domain and confers a gain of function. Preclinical trials in N659K mutant cell lines have shown sensitivity to multi-targeted tyrosine kinase inhibitors including imatinib and crenolanib.
BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway. BRAF G466V is a missense mutation which impairs BRAF kinase activity but paradoxically activates MEK and ERK through transactivation of c-RAF. This variant is associated with decreased cell proliferation and cell viability as compared to wild-type BRAF. This variant is a rare BRAF mutation and accounts for < 1% of BRAF mutations in colorectal adenocarcinoma. A single preclinical study of BRAF G466V in colon cancer demonstrated sensitivity to anti-EGFR tyrosine kinase therapy (cetuximab) and a MEK inhibitor (trametinib), however, there was no benefit seen with the RAF inhibitor vermurafinib. The clinicopathologic significance of BRAF G466V remains to be fully elucidated.
SMARCB1 is a member of the SWI/SNF chromatin remodeling complex and regulates transcription of several genes involved in cell proliferation. SMARCB1 R374Q does not lie within any known functional domains of the SMARCB1 protein. R374Q has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on protein function is unknown. SMARCB1 mutations are rare in colorectal adenocarcinomas and are reported in only about 1% of cases. The clinicopathologic significance of SMARCB1 variants in colorectal cancer remains to be further elucidated.
SMARCB1 is a member of the SWI/SNF chromatin remodeling complex and regulates transcription of several genes involved in cell proliferation. SMARCB1 mutations are rare in urothelial carcinomas and are found in about 2% of cases. SMARCB1 A203T is considered a variant of uncertain significance and has not been well classified in the literature. This variant has been reported a somatic mutation in a case of colon adenocarcinoma however this variant has also been reported a germline finding in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/25553173/). These results should be interpreted in the clinicopathologic context.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The K601E mutation results in an amino acid substitution at position 601 in BRAF, occurs within the highly conserved motif of the kinase domain. Most mutant BRAF proteins, such as K601E, have increased kinase activity and are transforming in vitro. BRAF mutations are infrequent in urothelial carcinoma and are identified in 3-5% of cases. Preclinical studies are investigating the use of MEK and RAS inhibitors in BRAF K601E mutant cell lines. The clinicopathologic effects of BRAF in this cancer type remain to be fully elucidated.
NRAS gene belongs to the family of RAS genes. It encodes a G protein that is important in the transmission of growth-promoting signals from the cell surface receptors to the nucleus through RAS-RAF- mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)-AKT cell signaling pathways. NRAS mutations are identified in multiple cancer types and tend in concentrate in codons 12, 13, and 61. NRAS mutations are rare in urothelial carcinomas of both the upper and lower urinary tract and are found in about 1% of cases. Currently, there are no direct anti-NRAS therapies available. The clinicopathologic significance of NRAS mutations in urothelial carcinoma remains to be further elucidated.
This gene encodes the catalytic subunit of DNA polymerase epsilon. The enzyme is involved in DNA repair and chromosomal DNA replication. Mutations in this gene have been associated with colorectal and endometrial cancer. P285R is the most common recurrent mutation of POLE in those types of cancers. Somatic POLE mutation is associated with approximately 3% of sporadic microsatellite-stable (MSS) but hypermutated CRCs.
The PTPN11gene encodes SHP-2, a widely expressed cytoplasmic protein tyrosine phosphatase. SHP-2 is essential for activation of the RAS/MAPK signaling cascade. Most mutations are gain-of-function and result in prolonged ligand-dependent activation of the RAS/MAPK cascade. Germ-line PTPN11 mutations cause Noonan syndrome, a developmental disorder characterized by an increased risk of malignancies. Activating somatic mutations in PTPN11 have been documented in certain hematologic malignancies but they are infrequent in solid tumors. About 3% of all lung cancers harbor somatic mutations in PTPN11 gene but their prognostic and therapeutic significance remains to be fully elucidated. The PTPN11 V497L variant identified in this case has not been characterized in the literature and therefore its effect on protein function is unknown. This variant is best classified as a variant of uncertain significance. The utility of SHP2 inhibitors continues to be explored in some preclinical studies.
The PTPN11gene encodes SHP-2, a widely expressed cytoplasmic protein tyrosine phosphatase. SHP-2 is essential for activation of the RAS/MAPK signaling cascade. Most mutations are gain-of-function and result in prolonged ligand-dependent activation of the RAS/MAPK cascade. Germ-line PTPN11 mutations cause Noonan syndrome, a developmental disorder characterized by an increased risk of malignancies. Activating somatic mutations in PTPN11 have been documented in certain hematologic malignancies but they are infrequent in solid tumors. The G503V variant results in increased phosphatase activity compared to the wild-type protein in culture. About 3% of all lung cancers harbor somatic mutations in PTPN11 gene but their prognostic and therapeutic significance remains to be fully elucidated. The utility of SHP2 inhibitors continues to be explored in some preclinical studies.
SMAD4 is a tumor suppressor gene and it encodes an intracellular mediator in the transforming growth factor b (TGF b) signal transduction pathway. SMAD4 mutations are very rare in glioblastoma and are present in less than 1% of cases and the significance of these mutations are unclear in this tumor type. The effect on protein function of SMAD4 P472T remains to be further elucidated. These results should be interpreted in the clinicopathologic context.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is mutated in a large number of cancers. It encodes a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Most PTEN mutations are loss-of-function mutations. Mono-allelic or bi-allelic loss of PTEN is found in a considerable fraction of tumors, including gliomas (75%). In glioblastoma, PTEN loss/deletion is associated with poor patient prognosis, and/or shorter disease-free survival. The PTEN P169H mutation, however, is not definitively known to cause a loss-of-function change in the PTEN protein and has been shown to confer a phosphatase activity similar to wild-type PTEN in yeast. This variant has been identified in one case of glioblastoma according to the literature. This result should be interpreted in the clinicopathologic context.
KIT, also known as proto-oncogene c-Kit or tyrosine-protein kinase Kit or CD117, is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of tissue types. Signaling through CD117 plays a role in cell survival, proliferation, and differentiation. KIT is found in approximately 1% of glioblastomas. The KIT D45N variant is in the extracellular domain, however, its effect on protein function is unknown. The clinical significance of KIT in glioblastoma and the clinicopathologic effect of this variant remains to be further elucidated.
CDH1 on 16q22.1 encodes E-cadherin which functions in intercellular adhesion. E-cadherin is involved in transmitting chemical signals and controlling cell maturation and movement, and acts as a tumor suppressor. CDH1 is rare in this tumor type and is found in approximately 1% of glioblastomas. The CDH1 A403T variant has not been characterized in the literature and therefore has an unknown effect on protein function and is best classified as a variant of uncertain significance (VUS). The clinical significance of CDH1 in glioblastoma is unknown and its clinicopathologic effect remains to be further elucidated.
NOTCH1 is a transmembrane receptor that plays a role in various cellular processes including cell fate determination, growth, and survival. NOTCH1 may be somatically mutated in a variety of cancers, and these mutations can be either gain- or loss-of-function mutations depending on the tumor type. Translocations and activating somatic mutations in NOTCH1 have been identified in T-cell acute lymphoblastic leukemia and chronic lymphocytic leukemia. On the other hand, NOTCH1 loss-of-function somatic mutations are more common in solid tumors, namely squamous cell carcinomas, and occur as missense, frameshift or nonsense mutations. Somatic NOTCH1 mutations are rare in lung adenocarcinoma and are found in about 4% of cases. The NOTCH1 L2457V variant identified in this case has been reported as a benign germline finding in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/380420/). These results should be interpreted in the clinical context.
The receptor tyrosine kinase FGFR2 is one of four fibroblast growth factor receptors designated FGFR1-4 that activate FGF signaling upon trans-autophosphorylation of the receptor dimers. Some genetic alterations of FGFR2 lead to aberrant activation of FGFR2 signaling cascades due to the creation of autocrine signaling loop or the release of FGFR2 from autoinhibition. Activating mutations, including FGFR2 N549K which lies within the protein kinase domain, have been associated with multiple types of malignancies. FGFR2 mutations are more common in tumors of hepatobiliary origin than other solid tumor locations and are found in about 7% of hepatobiliary adenocarcinomas. Treatments with pan-FGFR inhibitors and FGFR2 inhibitors have inhibited proliferation in some tumor types and are under investigation.
The protein encoded by the RB1 gene is a negative regulator of the cell cycle and was the first tumor suppressor gene identified. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Inactivation of RB1 and loss of RB1 tumor suppressor function has been identified in approximately 5% of hepatocellular carcinoma and is rare (<1%) in cholangiocarcinoma. RB1 R320* results in early truncation of the RB1 protein and presumably loss of function. The predictive and prognostic significance of RB1 mutations in adenocarcinoma of the liver is undergoing further investigation. It has been suggested that patients with RB1-deficient tumors do not respond to cyclin-dependent kinase (CDK) inhibitors; however, the clinical implication of the loss of a single copy of RB1, as in this patient's case, remains to be fully elucidated. These results should be interpreted in the clinical context.
The cytoplasmic b-catenin protein is implicated as a cell-cell adhesion regulator coupled with cadherin and is considered as a member in the wingless/Wnt signal transduction pathway. Mutations in CTNNB1, the gene encoding b-catenin, tend to impact or even eliminate APC-dependent serine and threonine phosphorylation sites in exon 3, resulting in oncogenic stabilization of the protein. Mutations in the b-catenin gene are uncommon in NSCLC occurring in about 1-4% of the cases. This particular variant has not been described lung adenocarcinomas but is located in a hotspot, thus likely to be oncogenic. Clinical correlation is recommended.
ERBB2 encodes HER2, a member of the epidermal growth factor (EGF) receptor family of receptor tyrosine kinases. ERBB2 mutations have been reported in ~12% of urothelial carcinomas. This particular variant I767M lies within the protein kinase domain of HER2 and has been shown to result in increased kinase activity in vitro. This variant has been identified in rare cases of urothelial carcinomas, among other cancer types, and is considered to be oncogenic. Further studies are needed to elucidate the role of anti-HER2 therapy in this setting. Clinical correlation is recommended.
FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes, and is mutated in several tumors including colorectal, liver, bladders and ovarian cancers. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. FBXW7 loss of function mutations have been described in many types of adenocarcinoma including colon, bladder and lung. FBXW7 mutations are present in approximately 7% of urothelial carcinomas. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin. However, this particular variant (H500Y) has not been characterized in the scientific literature. Therefore, the effect on protein function is unknown. Clinical correlation is recommended.
ATM alterations have been reported as germline variants which predispose to inherited cancer syndromes and as somatic (acquired) variants in tumors. ATM is part of many signalling networks, including cell metabolism and growth, oxidative stress, and chromatin remodelling, all of which can affect cancer progression. Although ATM is considered to be a tumour suppressor, ATM signaling may be advantageous to cancer cells in some settings, particularly in resistance to radio- and chemotherapeutic treatment. For this reason, the use of ATM inhibitors in cancer therapy is under exploration. Genetic alterations in ATM have been reported in ~15% of urothelial carcinomas. However, the significance of this particular variant (R2443Q) is unknown, according to ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/142211/)
PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways. PIK3CA mutations are present in ~5% of cutaneous melanomas. PIK3CA M1043I is a known oncogenic hotspot mutation. M1043I confers a gain of function on the protein as indicated by in increased activation of downstream signaling and and transformation in cell culture. Clinical trials targeting PI3K/Akt/mTor pathway inhibitors are available for patients with PIK3CA mutated tumors.
This is a cancer genes
MET amplification may be associated with sensitivity to MET inhibitors. MET amplification is associated with resistance to EGFR inhibitors in EGFR mutated lung cancer. MET alterations are commonly associated with papillary renal-cell carcinoma and it is very rare in clear cell renal cell carcinoma.
FGFR3 amplification may be associated with response to the multitargeted tyrosine kinase inhibitor pazopanib.
BCL2 genomic Amplification may be associated with sensitivity to BCL2 inhibitors, however these inhibitors are currently undergoing clinical trials and their efficacy and/or lack of toxicity has not yet been demonstrated.
ASXL1 regulates epigenetic functions including histone and chromatin modifications. ASXL1 mutations have been reported in 40-50% of chronic myelomonocytic leukemia(CMML), 20% of myelodsyplastic syndromes, 20-35% of primary myelofibrosis, 15% of systemic mastocytosis, 30% of patients with secondary acute myeloid leukemia and 5-10% of primary acute myeloid leukemia. ASXL1 mutations have also been described in CHIP and CCUS. In CMML, missense mutations of ASXL1 appear to be less common (less than 10% of cases). Nonsense and frameshift mutations (but apparently not missense mutations) of ASXL1 have been reported to carry an adverse prognostic impact in cases of chronic myelomonocytic leukemia. In addition, ASXL1 mutations have been associated with adverse outcome in myelodysplasia, primary myelofibrosis and systemic mastocytosis. Among cases of AML, ASXL1 mutations appear to be associated with adverse prognosis in some subtypes of AML according to some, but not all, studies. ASXL1 mutations may coexist with mutations of splicing factor components, TET2 and RUNX1; for example, co-existence of U2AF1 and ASXL1 mutations have been described in CMML and primary myelofibrosis; While in AML, ASXL1 mutations have been reported to be exclusive of NPM1 mutations according to some studies.
BCOR is a ubiquitously expressed nuclear protein that is a transcriptional corepressor important in several cellular processes. Somatic, nonsense and frameshift mutations throughout BCOR have been reported in approximately 7% of chronic myelomonocytic leukemia, 4% of patients with myelodysplastic syndrome(MDS), 4% of primary acute myeloid leukemia and appear to be associated with RUNX1 and DNMT3A mutations . Also, BCOR mutations may be enriched among cases of AML lacking NPM1, CEBPA, FLT3-ITD, IDH1 and MLL-PTD alterations. BCOR mutations tend to be subclonal in MDS, clonal in primary AML and are believed to have significance as loss of function mutations in a tumor suppressor gene that affect the functional allele in male and female patients. The presence of BCOR mutation in patients with MDS and AML has been associated with poorer overall survival according to some studies.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in up to 100% of Hairy cell leukemia, 40-70% of Langerhans cell histiocytosis, approximately 50% of Erdheim-Chester disease, approximately 5% of diffuse large B cell lymphoma and plasma cell neoplasms and less than 5% of chronic lymphocytic leukemia. Some types of Hairy Cell Leukemia (eg, Hairy Cell Leukemia-Variant, Hairy Cell Leukemia with IgHV4-34 rearrangement) are negative for BRAF V600E mutation and may have MAP2K1 mutations. While some reports have found that 10-20% of cases of acute leukemias (ALL or AML) may have BRAF mutations, other reports have described no BRAF in those diseases or in myeloid diseases such as MDS or CML. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). B-Raf inhibitors(eg, Vemurafenib) have been FDA approved for therapy for various tumor types and have been used in Hairy Cell Leukemia in some clinical settings, including in combination with other therapy.
BRINP3(FAM5C) has been reported to be mutated in <10% of some types of AML.
TP53 encodes p53, a tumor suppressor protein that consists of transactivation domain, proline-rich domain, DNA-binding domain, oligomerization domain, and regulatory domain. p53 responds to diverse cellular stresses to maintain genomic stability and to induce cell cycle arrest, apoptosis, DNA repair and metabolic changes. TP53 mutations represent an important mechanism of resistance to DNA-damaging chemotherapeutic agents. Somatic TP53 mutations are found in a variety of cancers with various frequencies depending on cancer type; overall, TP53 is mutated in over one-half of human cancers. Missense mutations were the most frequent (~70-80%), followed by frameshift and nonsense mutations. Most TP53 mutations are clustered in the DNA-binding domain encompassing exons 5 and 8. These mutations either directly disrupt the DNA-binding domain of TP53 or cause conformational changes of the TP53 protein, thus leading to severely impaired TP53 function. Overall in myeloid malignancies, TP53 mutations are found in 5% to 15% of de novo MDS and AML but 20% of myelodysplastic syndrome with isolated del(5q) and ~50% of MDS/AML with complex karyotype. TP53 mutations are also more frequent in therapy-associated myeloid neoplasm (21-38%) compared to de novo MDS and AML. TP53 mutations are also found in 8% of blastic plasmacytoid dendritic cell neoplasm, and less than 5% in myeloproliferative neoplasms (ET, PV and PMF) and chronic myelomonocytic leukemia. TP53 mutations are independently associated with a poor prognosis in myelodysplastic syndrome (NCCN Guidelines for Myelodysplastic Syndromes) and is a poor risk factor in AML (NCCN Guildelines for AML). TP53 mutations are also associated with resistance to lenalidomide or relapse during lenalidomide treatment. TP53 mutations are independently associated with unfavorable outcomes and shorter survival after hematopoietic stem cell transplantation in patients with myelodysplastic syndrome and myelodysplastic syndrome/acute myeloid leukemia, but an increased response to decitabine in patients with myelodysplastic syndrome or acute myeloid leukemia.
SUZ12 is one of the core components of the polycomb repressive complex 2 (PRC2), which is a highly conserved histone H3 lysine 27 methyltransferase that regulates the expression of developmental genes. SUZ12 mutations are present infrequently (<2%) in myeloproliferative neoplasms (MPN) and myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN). The mutations are missense and tend to be located at the highly conserved VEFS domain, is required for the interaction between SUZ12 and EZH2. These mutations reduced PRC2 histone methyltransferase activity in vitro. Inactivating mutations of the catalytic component of PRC2, EZH2, can also be seen in myeloid neoplasms. Mice with loss of function mutations in PRC2 components display enhanced activity of their hematopoietic stem cell/progenitor population and loss of SUZ12 function in particular enhances hematopoietic stem cell activity.
NFE2 codes for a subunit of the NF-E2 (nuclear factor, erythroid 2) complex essential for regulating erythroid and megakaryocytic maturation and differentiation. This submit regulates a number of erythroid and megakaryocytic promoters. Rare insertion and deletion mutations leading to premature translation termination in NFE2 were found in 2% of myeloproliferative neoplasms (MPN). NFE2 mutatoins appear to be enriched in isolated myeloid sarcomas (MS). Of the six investigated cases of MS without previous or concurrent AML in the bone marrow, 4 (67%) harbored mutations in NFE2, 3 of which were missense and 1 of which was frameshift. In addition, NFE2 is overexpressed in the majority of patients with MPNs. In murine models, over-expression of NFE2 caused an MPN phenotype with spontaneous leukemic transformation, supporting a direct role of NFE2 in the pathogenesis of MPN. Over-expression of NFE2 in MPN may be attributed to histone H3Y41 phosphorylation by V617F-mutated JAK2 and transcriptional activation of NFE2 by JMJD1C in a positive feedback loop.
ETV6 is a transcriptional repressor and is frequently involved in translocations with a variety of different partner genes in a range of hematologic malignancies. Mutations of ETV6 have been described in <5% of myelodysplastic syndromes and appear to be more frequent (ie, 10-24% of cases) in early T cell precursor type (immature) acute lymphoblastic leukemias. In addition, ETV6 mutations have been reported in association with hereditary myeloid disorders. These mutations occur throughout the gene and typically correspond to loss of function mutations (nonsense and frameshift mutations). ETV6 mutations may occasionally occur in a homozygous/hemizygous manner and tend to occur with mutations in NOTCH1 in lymphoblastic leukemia. In MDS, ETV6 mutations have been independently associated with an adverse prognosis. If clinical findings and family history are concerning for the presence of an inherited disorder, then genetic counseling may be helpful, if clinically indicated.
EZH2 encodes the histone methyltransferase subunit of the polycomb repressive complex 2 (PRC2) that leads to H3K27me3 and promotes transcriptional repression. EZH2 loss of function mutations (nonsense, frameshift mutations, occasionally occurring as homozygous mutations) may occur throughout the gene and have been reported in less than 10% of patients with acute myeloid leukemia, myelodysplasia, atypical chronic myelogenous leukemia, primary myelofibrosis and up to 12% of patients with chronic myelomonocytic leukemia. EZH2 loss of function mutations may be more frequent (15%) among cases of T cell acute lymphoblastic leukemia. EZH2 mutations have been independently associated with adverse prognosis in MDS and MDS/MPN. Therapeutic targeting of EZH2 is currently under study for some types of lymphoma and solid tumors.
HNRNPK maps to the 9q21.32 locus, and deletion of this locus, along with an associated reduction in HNRNPK expression, has been reported in patients with acute myeloid leukemia (AML). HNRNPK mutations have also been reported in AML.
KDM6A is a histone demethylase. In a recent study, KDM6A was noted to be a recurrently altered gene in a subset of relapsed AML cases and may represent a mechanism of cytarabine resistance. These alterations include partial gene deletions and mutations that lead to decreased KDM6A expression/function.
NOTCH1 is a transmembrane receptor, which plays a role in cell fate determination, growth, and survival. Notch signaling has been demonstrated to play a role in lung development and lung carcinogenesis. Notch activity is counteracted by NUMB. Gain-of-function mutations of NOTCH1 have been identified in approximately 10% of patients with non-small cell lung carcinoma (NSCLC). In addition, loss-of-function mutations in NUMB that allow for increased NOTCH1 activity have been observed in approximately 30% of NSCLC patients. Studies have observed that increased NOTCH1 expression is associated with a poor prognosis in patients with lung adenocarcinoma. The NOTCH1 intronic deletion variant (NM_017617:g.139397792_139397795del) is located nine base pairs downstream of exon 27. While the variant is located in close proximity to an exon-intron junction, a potential effect on gene splicing is unknown. These results should be interpreted in the clinical context.
ATM is a member of the protein superfamily of phosphatidylinositol 3-kinase related serine/threonine kinases (PIKKs). ATM functions as a tumor suppressor that initiates DNA damage checkpoint signaling. Germline loss-of-function mutations in ATM have been identified in the autosomal recessive disorder Ataxia telangiectasia. Somatic mutations in ATM have been identified in lymphoid malignancies and a selection of solid tumors. ATM-mutant cancers are increasingly sensitive to DNA damaging agents due to deficits in DNA repair pathways, and ATM loss may result in better response to checkpoint inhibition in some cancers. Genetic alterations of ATM have been identified in approximately 10% of lung adenocarcinomas. One study predicted impaired ATM kinase activity in the setting of ATM R2691C mutation based on structural modeling; however, these results have not been validated biochemically. Of note, this variant is reported in ClinVar as a germline variant of uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/133636/). Correlation with other clinical and lab findings is recommended.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Various B-Raf inhibitors(Vemurafenib, Dabrafenib) have been FDA approved for therapy for some tumor types in certain settings, and clinical trials for advanced BRAF V600 mutation-positive tumors using targeted therapy (often in combination with other therapy) may be available (clinical trials.gov). It has been found that BRAF V600E has a mutation frequency of 2% in pancreatic cancer. A small study showed that no BRAF mutations were present in cases without KRAS mutations and in the few cases with BRAF mutations, a KRAS mutation was also present.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is mutated in a large number of cancers. It encodes a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Cancer-associated alterations in this gene often result in loss of PTEN protein and upregulation of the PI3K/AKT/mTOR pathway. PTEN mutations have been reported in 15% of anaplastic thyroid cancer. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome. Patients with Cowden syndrome have an increased risk of developing epithelial thyroid cancer, follicular carcinoma being the most common, of up to 10% compared to <1% in the general population. The PTEN I101T has been observed in a variety of cancer types. One study identified the PTEN I101T variant in 1 out of 172 patients with germ line PTEN mutations. Of note, an in vitro studied observed that the PTEN I101T variant reduced the half-life of PTEN as well as significantly reduced its activity. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.
BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. The hotspot for mutations in BRAF is at codon Val600 and these are activating mutations. The most common activating mutation is p.Val600Glu(V600E). Activating BRAF(V600E) (Val600Glu) mutations have been identified in approximately 1-2% of lung adenocarcinomas. Various BRAF inhibitors (Vemurafenib, Dabrafenib, and Trametinib) have been FDA approved for therapy for some tumor types in certain clinical settings. Of note, Dabrafenib and Trametinib are approved for metastatic non-small cell lung cancer (NSCLC) harboring BRAF V600E mutations.
CDH1 on 16q22.1 encodes E-cadherin which functions in intercellular adhesion. E-cadherin is involved in transmitting chemical signals and controlling cell maturation and movement, and acts as a tumor suppressor. A lack of functional E-cadherin impairs cell adhesion and increases the likelihood of invasion and metastasis of tumor cells. CDH1 is altered by mutation or deletion in various cancers and loss of E-cadherin has been demonstrated in a variety of sporadic cancer types including breast cancer, gastric cancer, colorectal cancer, and esophageal cancer. Along with point mutations and loss of heterozygosity (LOH), epigenetic silencing by hypermethylation of the CDH1 promoter has been associated with the loss of E-cadherin gene expression during cancer progression. Individuals with a germline CDH1 mutation have an increased risk of developing diffuse gastric cancer and breast cancer. More than 100 different pathogenic germline mutations are distributed throughout the CDH1 gene including splice-site sequences and have been found to cause a familial cancer disorder called hereditary diffuse gastric cancer (HDGC). Somatic CDH1 alterations are also found in approximately 30% of all patients with gastric cancers, both diffuse and intestinal types. Genetic alterations of CDH1 have been identified in 4% of colorectal adenocarcinomas. CDH1 D400V lies within the Cadherin domain 3 of the Cdh1 protein (UniProt.org) and mutations in this locus has been reported previously.
CTNNB1 encodes the protein b-catenin, a transcriptional activator involved in the WNT signaling pathway. Somatic gain-of-function mutations in CTNNB1 result in aberrant accumulation of the b-catenin protein and are prevalent in a wide range of solid tumors, including endometrial carcinoma, ovarian carcinoma, hepatocellular carcinoma, and colorectal carcinoma, among others. Cancers with CTNNB1 mutations are presumed to be resistant to pharmacologic inhibition of upstream components of the WNT pathway, instead requiring direct inhibition of b-catenin function. Genetic alterations in CTNNB1 have been identified in 4% of non-small cell lung cancers. The CTNNB1 S45F mutation is likely oncogenic. No real progress has been made in targeting oncogenic mutant forms of CTNNB1 in lung cancer.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is commonly mutated in a large number of cancers. It negatively regulates intracellular levels of phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Approximately 20-30% of colorectal carcinomas involve biallelic inactivation of PTEN through a combination of genetic and epigenetic mechanisms. The R15I missense mutation falls within the PIP2 binding motif in the phosphatase domain of PTEN, which involves residues 6-15. PTEN R15I has been show to result in loss of phosphatase activity in vitro. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.
KDR encodes the protein VEGF2, a receptor tyrosine kinase that regulates angiogenesis and vascular development. While KDR mutations are rare, amplification or protein overexpression have been reported in small proportion of a variety of solid tumors. It is unclear if KDR mutation plays a role in colorectal carcinoma pathogenesis; however, it may have a role in clinical outcome prediction and therapeutic response. For example, increased expression of VEGFA, FLT1, and KDR in colorectal carcinoma is associated with a poor prognosis and lack of response to bevacizumab therapy. Although the functional consequence of KDR K270N has not been characterized, it has been reported previously as a somatic variant in in colorectal carcinomas. These results should be interpreted in the clinical context. Most therapies blocking KDR signaling target the angiogenesis pathway in general, such as bevacizumab, an antibody that targets VEGF-A.
KIT (CD117) is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of human tissues. Gain-of-function mutations of the KIT gene have been identified that produce ligand-independent activation of KIT and cell proliferation. KIT receptor and its ligand have been demonstrated in human colon cancer cell lines. Some studies have shown high frequency of KIT overexpression in stage II colon cancer patients (59.3%) with significant correlation between KIT overexpression and reduced disease free survival. However, other studies failed to demonstrate KIT expression in a significant number of colorectal cancers suggesting that KIT kinase activation is not a prominent pathogenetic feature of colorectal cancers. Role of KIT continues to be studied in colon cancers. KIT K807N missense mutation is known to be oncogenic. Several tyrosine kinase inhibitors against KIT are available, mainly for gastrointestinal stromal tumors and melanoma. The role of these targeted therapies in colorectal carcinomas need to be further elucidated.
Somatic mutations in PIK3CA have been found in 10--30% of colorectal cancers. KRAS, NRAS, BRAF and PIK3CA and non-functional PTEN predict resistance to anti-EGFR therapies in metastatic colorectal cancer. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use may be associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation may be a molecular biomarker that predicts response to aspirin therapy. The R88Q mutation falls within the ABD domain of the p110a catalytic subunit and has been shown to result in gain-of-function in vitro. PIK3CA may be a target of directed therapy in some clinical settings.
KDR (kinase domain receptor), also known as VEGFR2 or Flk-1, is a tyrosine kinase receptor for vascular endothelial growth factor (VEGF) and plays a key role in angiogenesis. While KDR mutations are rare, amplification or protein overexpression have been reported in small proportion of a variety of solid tumors. Genetic alteration in KDR have been identified in 10% of lung adenocarcinomas. KDR (VEGFR2) R962H lies within the protein kinase domain of the KDR. This variant has not been biochemically characterized; however, mutations in this locus have been identified in various tumor types. Most therapies blocking KDR signaling target the angiogenesis pathway in general, such as bevacizumab, an antibody that targets VEGF-A. These results should be interpreted in the clinical context.
BRAF is a serine/threonine kinase that plays a key role in the regulation of the mitogen-activated protein kinase (MAPK) cascade. Genetic alterations in BRAF are found in a large percentage of melanomas, thyroid cancers and histiocytic neoplasms as well as a small fraction of lung and colorectal cancers. Somatic mutations in BRAF have been found in up to 10% of all NSCLC, more common in adenocarcinomas. Genetic alterations of BRAF have been identified in 9% of lung adenocarcinomas. BRAF N581I lies within the protein kinase domain of the Braf protein (UniProt.org). N581I results in low Braf kinase activity and Ras-dependent activation of Erk signaling in cell culture but, induces similar cell proliferation and cell viability as wild-type Braf. The BRAF N581I mutation is known to be oncogenic.
BRAF is a serine/threonine kinase that plays a key role in the regulation of the mitogen-activated protein kinase (MAPK) cascade. Genetic alterations in BRAF are found in a large percentage of melanomas, thyroid cancers and histiocytic neoplasms as well as a small fraction of lung and colorectal cancers. Somatic mutations in BRAF have been found in up to 10% of all NSCLC, more common in adenocarcinomas. Genetic alterations of BRAF have been identified in 9% of lung adenocarcinomas. E586 is located within the kinase domain of BRAF and E586K mutation has been shown to result in increased kinase activity. The BRAF E586K mutation is likely oncogenic although the predictive and prognostic significance of this mutation needs further study. Correlation with other laboratory and clinical findings is recommended.
FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. FBXW7 R505C lies within the WD4 repeat region and confers a loss of FBXW7-substrate interaction and impairs substrate degradation by FBXW7, resulting in sustained NICD and MYC expression. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin. A single study has reported only limited activity in phase I trials using mTOR inhibitors in patients with advanced cancers including colorectal cancer. The clinical utility remains unknown.
FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes and is inactivated by mutation in various cancers, most frequently in endometrial and colorectal cancers. Substrates of FBXW7 include the proteins c-MYC, mTOR, NOTCH1, cyclin-E, and JUN, which are instrumental in the regulation of cell division, differentiation and growth, and which are often inappropriately activated in cancer. Inactivation of FBXW7 by mutation or copy number loss results in aberrant accumulation of the above oncoproteins, which subsequently contributes to malignant transformation. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. Most mutations in FBXW7 are point mutations that disrupt substrate binding, while <10% are small deletions or insertions. FBXW7 is altered in 17% of colorectal adenocarcinomas. The FBXW7 R465H variant is considered to be likely oncogenic. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin. A single study has reported only limited activity in phase I trials using mTOR inhibitors in patients with advanced cancers including colorectal cancer. The clinical utility remains unknown.
SMAD4 encodes a tumor suppressor and transcription factor that is a downstream effector in the TGF-ss signal transduction pathway. Germline mutations in SMAD4 have been associated with juvenile polyposis syndrome. SMAD4 is mutated in one third of colorectal cancer and half of pancreatic tumors. Genetic alterations in SMAD4 have been identified in 33% of pancreatic adenocarcinomas. SMAD4 inactivation by allelic deletion or mutation mainly occurs in late stage pancreatic ductal adenocarcinoma and is associated with poorer prognosis. SMAD4 D351G lies at a hotspot residue within the MH2 domain of the Smad4 protein (UniProt.org). D351G has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on Smad4 protein function is unknown. The SMAD4 D351H variant has been described in human colorectal cancer cell lines and reported as likely oncogenic, suggesting that the D351G variant is also likely to be oncogenic. SMAD4 loss has been found to increase resistance to the chemotherapeutic agent 5'-fluorouracil.
The catalytic subunit (p110a) of phosphatidylinositol-3-kinase (PI3K) is encoded by the PIK3CA gene and acts to activate several signaling cascades, including the well-characterized AKT-mTOR pathway that promotes cell survival, proliferation, growth and motility. PIK3CA is among the most commonly mutated genes in cancer and aberrant activation of PI3K is a transforming event. Somatic mutations in PIK3CA have been found in 1--3% of NSCLC and genetic alteration in PIK3CA have been identified in 7% of lung adenocarcinomas. These mutations typically occur within specific hotspot regions. PIK3CA mutations appear to be more common in squamous cell histology compared to adenocarcinoma and can occur with or without a history of smoking. PIK3CA mutations can co-occur with EGFR mutations and PIK3CA mutations have been detected in a small percentage (approximately 5%) of EGFR-mutated lung cancers with acquired resistance to EGFR TKI therapy. The PIK3CA H1047R mutation is known to be oncogenic.
The proto-oncogene KIT encodes a type 3 transmembrane receptor tyrosine kinase. c-kit (CD117) is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of human tissues. Gain-of-function mutations of the c-kit gene have been identified that produce ligand-independent activation of c-kit and cell proliferation. Some of these mutations appear causative in the pathogenesis of adult mastocytosis and most gastrointestinal stromal tumors (GISTs). Activating KIT mutations occur in 80 - 90% of GISTs and several small molecule tyrosine kinase inhibitors (TKIs) targeting KIT that have been approved by the US Food and Drug Administration with the efficacy of each TKI strongly depending on the location of the activating KIT mutation. c-kit receptor and its ligand have been demonstrated in human colon cancer cell lines. Some studies have shown high frequency of c-Kit overexpression in stage II colon cancer patients (59.3%) with significant correlation between c-Kit overexpression and reduced disease free survival. However, other studies failed to demonstrate c-kit expression in a significant number of colorectal cancers suggesting that c-kit kinase activation is not a prominent pathogenetic feature of colorectal cancers. The role of c-Kit continues to be studied in colon cancers. The KIT D52N mutation likely represent an oncogenic gain of function mutation.
KRAS, member of the RAS family of small GTPases which functions as an upstream regulator of the MAPK and PI3K pathways, is frequently mutated in a diverse range of cancers including pancreatic, colorectal and lung cancers. More than 90% of pancreatic ductal adenocarcinoma samples have a KRAS mutation which may have prognostic, and (with ongoing trials assessing the efficacy of novel KRAS inhibitors) possibly therapeutic implications. However, targeting KRAS directly has been difficult in these tumors. KRAS mutations are infrequent in gastric carcinomas and have been reported in approximately 6% of cases. The gain of function KRAS G12D mutation is known to be oncogenic.
The catalytic subunit of phosphatidylinositol-3-kinase (PI3K) is encoded by the PIK3CA gene. PIK3CA is among the most commonly mutated genes in cancer and aberrant activation of PI3K is a transforming event. PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways. The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains), with three hotspots (E542K, E545K, and H1047R/L). PIK3CA mutations have been reported in various tumor types including up to 36% and 11% of hepatocellular carcinoma and gastric cancer, respectively. They are detected less frequently in cholangiocarcinoma (~6%) and pancreatic adenocarcinoma (~4%). The predictive and prognostic significance of PIK3CA mutations is unclear and needs further elucidation. Clinical trials targeting PI3K/Akt/mTor pathway inhibitors are available for patients with PIK3CA mutated tumors. The PIK3CA N1044K mutation is known to be oncogenic.
The GNAS gene encodes the stimulatory G-alpha subunit of the heterotrimeric guanine nucleotide-binding protein (G-protein) membrane complex. Activating mutations in GNAS that have been linked to the endocrine hyperplasia of McCune-Albright syndrome have also been found in growth-hormone-secreting pituitary tumors. Point mutations in the GNAS gene, many of which involve the residues R201 and Q227, can lead to constitutive signaling activity, resulting in cellular proliferation and oncogenesis. Tumor types that have been found to harbor GNAS mutations include colon, parathyroid, and ovarian cancers, hepatocellular carcinoma, and pancreatic intraductal papillary mucinous neoplasms. The GNAS R201C mutation is known to be oncogenic.
SMAD4 encodes a tumor suppressor and transcription factor that is a downstream effector in the TGF-ss signal transduction pathway. Germline mutations in SMAD4 have been associated with juvenile polyposis syndrome (JPS). Loss of SMAD4 expression or somatic mutations in SMAD4 are found in pancreatic cancer and are associated with tumor grade. Somatic alterations in SMAD4 are observed at lower frequencies in multiple tumor types, including colon and lung adenocarcinoma. SMAD4 R361C lies at a hotspot residue within MH2 domain of the Smad4 protein (UniProt.org). R361C confers a loss of function to the Smad4 protein as demonstrated by reduced Smad4 transactivating activity in cell assays. The SMAD4 R361C mutation is likely oncogenic. Studies of loss of function somatic mutations and studies of loss of heterozygosity (LOH) at the SMAD4 locus have shown an association with poor prognosis. There are ongoing clinical trials for colorectal tumors harboring SMAD4 alterations.
PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways. The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains), with three hotspots (E542K, E545K, and H1047R/L). PIK3CA mutations have been reported in various tumor types including up to 36% and 11% of hepatocellular carcinoma and gastric cancer, respectively. They are detected less frequently in cholangiocarcinoma (~6%) and pancreatic adenocarcinoma (~4%). The predictive and prognostic significance of PIK3CA mutations in adenocarcinoma of the small intestine is unclear and needs further elucidation. Clinical trials targeting PI3K/Akt/mTor pathway inhibitors are available for patients with PIK3CA mutated tumors.
The Mesenchymal Epithelial Transition (MET) proto-oncogene encodes the MET receptor tyrosine kinase, also called c-MET or hepatocyte growth factor (HGF) receptor. MET is a ubiquitously expressed cell surface receptor that leads to the activation of several downstream intracellular pathways which promote cellular growth and proliferation, motility, migration and angiogenesis. Dysregulation of MET via gene amplification, germline or somatic mutations or receptor overexpression has been observed in a variety of epithelial cancers, including breast prostate cancer, non-small cell lung cancer, renal papillary carcinoma, hepatocellular and gastric carcinomas. Genetic alterations in MET have been identified in 0.4% of thyroid carcinomas. The prognostic and predictive significance of MET mutations in thyroid cancer is not clear and correlation with other clinical and laboratory findings is necessary. M362T has been identified in the scientific literature, but has not been biochemically characterized and therefore, its effect on protein function is unknown. This variant is reported as a benign/likely benign germline variant in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/93565).
SMAD4 is a transcription factor that functions as a critical effector in the transforming growth factor beta (TGFss) signal pathway that controls cellular proliferation, differentiation and tissue homeostasis. The TGFss pathway suppresses tumorigenesis in premalignant states and promotes invasiveness and metastasis during cancer progression. Germline mutations in SMAD4 have been associated with juvenile polyposis syndrome (JPS). Somatic alterations in SMAD4 are in multiple tumor types, including colon and lung adenocarcinoma. SMAD4 inactivation by allelic deletion or mutation mainly occurs in late stage pancreatic ductal adenocarcinoma and is associated with poorer prognosis. SMAD4 loss increased resistance to the chemotherapeutic agent 5'-fluorouracil. The identified deletion is not characterized but is present at a site of frequent mutations and is potentially oncogenic. The role of SMAD4 variants in small intestinal adenocarcinomas need further characterization. Clinical correlation is recommended.
BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and V600E is an activating mutation of BRAF. The BRAF V600E mutation has been reported in 45% of patients with papillary thyroid carcinoma, which comprise 80 % of all thyroid cancers. Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC, other thyroid neoplasms, or nodular goiters. Anaplastic thyroid carcinomas are rare, highly aggressive, undifferentiated tumors that comprise 1% to 2% of all thyroid cancers in the United States. Well-differentiated papillary thyroid cancer, in which BRAF V600 mutations are an early and common driver mutation, precedes or coexists with approximately 50% of anaplastic thyroid carcinomas. Between 20% and 50% of anaplastic thyroid carcinomas harbor activating BRAF V600 mutations, with unknown prognostic significance. The possible prognostic impact of BRAF V600E mutations in carcinoma of the thyroid continues to be studied.
CDH1 on 16q22.1 encodes E-cadherin which functions in intercellular adhesion. E-cadherin is involved in transmitting chemical signals and controlling cell maturation and movement, and acts as a tumor suppressor. A lack of functional E-cadherin impairs cell adhesion and increases the likelihood of invasion and metastasis of tumor cells. CDH1 is altered by mutation or deletion in various cancers and loss of E-cadherin has been demonstrated in a variety of sporadic cancer types including breast cancer, gastric cancer, colorectal cancer, and esophageal cancer. Along with point mutations and loss of heterozygosity (LOH), epigenetic silencing by hypermethylation of the CDH1 promoter has been associated with the loss of E-cadherin gene expression during cancer progression. Individuals with a germline CDH1 mutation have an increased risk of developing diffuse gastric cancer and breast cancer. More than 100 different pathogenic germline mutations are distributed throughout the CDH1 gene including splice-site sequences and have been found to cause a familial cancer disorder called hereditary diffuse gastric cancer (HDGC). Somatic CDH1 alterations are also found in approximately 30% of all patients with gastric cancers, both diffuse and intestinal types. Genetic alterations of CDH1 have been identified in 4% of colorectal adenocarcinomas. CDH1 D400V lies within the Cadherin domain 3 of the Cdh1 protein (UniProt.org). D400V has not been characterized in the scientific literature and therefore, its effect on CDH1 protein function is unknown.
ATM is a member of the protein superfamily of phosphatidylinositol 3-kinase related serine/threonine kinases (PIKKs). ATM is part of many signaling networks, including cell metabolism and growth, oxidative stress, and chromatin remodeling, all of which can affect cancer progression. Although ATM is considered to be a tumor suppressor, ATM signaling may be advantageous to cancer cells in some settings, particularly in resistance to radio- and chemotherapeutic treatment. Germline ATM mutations are the defining feature of ataxia telangiectasia syndrome, a rare, neurodegenerative, autosomal disorder. ATM somatic mutations are associated with endometrial, colon, pancreatic, breast cancers and urothelial cancers. ATM-mutant cancers are increasingly sensitive to DNA damaging agents due to deficits in DNA repair pathways, and ATM loss may result in better response to checkpoint inhibition in some cancers. For this reason, the use of ATM inhibitors in cancer therapy is under exploration. Genetic alterations of ATM have been identified in 5% of pancreatic adenocarcinomas. ATM F858L has been identified in the scientific literature, but has not been biochemically characterized and therefore, its effect on ATM protein function is unknown. According to ClinVar, this variant is considered to be a benign/likely benign germline variant (https://preview.ncbi.nlm.nih.gov/clinvar/variation/132736/). Clinical correlation is recommended.
FGFR3 is one of four high affinity tyrosine kinase receptors for the fibroblast growth factor family of ligands. On ligand stimulation, FGFR3 undergoes dimerization and tyrosine autophosphorylation, resulting in cell proliferation or differentiation through the mitogen-activated protein kinase (MAPK) and phospholipase Cg signal transduction pathways. Some FGFR3 mutations are believed to result in ligand-independent activation of the receptor. However, FGFR3 F384L mutation is not associated with activation of FGFR and, in NIH-3T3 cells, it was demonstrated to be devoid of any transforming activity. FGFR3 is altered in 2.9% of pancreatic adenocarcinomas. The FGFR3 F384L mutation has been reported as a benign/likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/134404/). Clinical correlation is recommended.
PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways. The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exons 9 and 20 (helical and kinase domains), with three hotspots (E542K, E545K, and H1047R/L). PIK3CA mutations have been reported in various tumor types including up to 36% and 11% of hepatocellular carcinoma and gastric cancer, respectively. They are detected less frequently in cholangiocarcinoma (~6%) and pancreatic adenocarcinoma (~4%). The predictive and prognostic significance of PIK3CA mutations is unclear and needs further elucidation. Clinical trials targeting PI3K/Akt/mTor pathway inhibitors are available for patients with PIK3CA mutated tumors.
CTNNB1 encodes b-catenin, a transcriptional co-regulator and an adapter protein for cellular adhesion involved in the WNT signaling pathway. Somatic gain-of-function mutations in CTNNB1 result in aberrant accumulation of the b-catenin protein and are prevalent in a wide range of solid tumors, including uterine/endometrial carcinoma, ovarian, hepatocellular carcinoma, and colorectal carcinoma, among others. CTNNB1 mutations are particularly common in colorectal carcinomas associated with hereditary non-polyposis colon cancer syndrome and wild type APC gene, and are extremely rare in sporadic colorectal cancers. CTNNB1 is altered in 2.9% of pancreatic adenocarcinomas. The CTNNB1 T41A mutation is known to be oncogenic. Preclinical studies suggest that CTNNB1 mutations may confer resistance to PI3K-AKT inhibitors in colorectal cancer. Cancers with CTNNB1 mutations are presumed to be resistant to pharmacologic inhibition of upstream components of the WNT pathway, instead requiring direct inhibition of b-catenin function. The role of CTNNB1 mutations in pancreatic adenocarcinomas requires further elucidation.
The STK11 is a tumor suppressor gene located on chromosome 19p13.3. The encoded protein has serine--threonine kinase activity. Functionally, STK11 regulates cellular energy metabolism and cell polarity by activating AMP-activated protein kinase (AMPK) and other members of the AMPK family. Germline mutations in the STK11 gene are responsible for Peutz--Jeghers syndrome, an autosomal dominant disorder with variable clinical phenotype and increased risk of some cancers. Somatic inactivating mutations of STK11 gene are reported in several tumors. Clinical relevance of these alterations and impact on disease progression and patient survival needs to be fully elucidated.
PTEN is a lipid and protein phosphatase that negatively regulates the PI3K/AKT/mTOR pathway. Cancer-associated alterations in this gene often result in loss of PTEN protein and upregulation of the PI3K/AKT/mTOR pathway. PTEN mutations have been reported in ~2% of head and neck squamous cell carcinomas and 15% of anaplastic thyroid carcinomas. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome. This particular variant M134I has been reported as a likely pathogenic germline variant (ClinVar, https://preview.ncbi.nlm.nih.gov/clinvar/variation/428267/) and has also been reported as a somatic variant. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.
B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in <2% of head and neck squamous cell carcinomas. The hotspot for mutations in BRAF is at codon Val600 and the most common one is p.Val600Glu (V600E). Various B-RAF inhibitors have been FDA approved for cancer therapy in certain settings.
PTEN is an obligate haplo-insufficient tumor suppressor gene and is mutated in a large number of cancers. It encodes a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. PTEN mutations are loss-of-function mutations and occur in 3% of urothelial carcinomas. The above variants (R130Q and G165R) are predicted to result in loss of function based on preclinical in vitro studies. Whether PTEN alterations predict for responsiveness to mTORC1 inhibitors is less certain at this time.
Beta catenin is a transcriptional co-regulator and an adapter protein for cellular adhesion; it comprises part of the Wnt signaling pathway and intracellular levels of beta-catenin are regulated by its phosphorylation, ubiquitination and proteosomal degradation. Accumulation of nuclear beta catenin can lead to a tumoral phenotype and oncogenic transformation in a variety of solid tumors. Various oncogenic mutants of beta catenin have been found in different tumor types which alter its degradation, leading to its accumulation and promoting tumor growth. CTNNB1 mutations in prostate cancer occur rarely, in only 2-5% of cases. Currently, the function of b-Catenin in human prostate cancer continues to be explored. In the context of prostate, b-Catenin may modulate the androgen receptor (AR) pathway. This particular variant S33F is predicted to confer a gain of function to the CTNNB1 protein as demonstrated by nuclear accumulation of CTNNB1. Clinical correlation is recommended.
KIT, also known as proto-oncogene c-Kit or tyrosine-protein kinase Kit or CD117, is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of tissue types. Signaling through CD117 plays a role in cell survival, proliferation, and differentiation. Altered forms of this receptor may be associated with many types of cancers including hematopoietic malignancies, gastrointestinal stromal tumors, and various carcinomas and sarcomas. KIT G565V lies within the cytoplasmic domain of the Kit protein; this variant has been documented in the scientific literature (in melanoma). While its effect on Kit protein function is unknown, it is reported in ClinVar as likely benign germline variant (https://preview.ncbi.nlm.nih.gov/clinvar/variation/41600/).
JAK2 is a non-receptor tyrosine kinase that mediates signaling via the JAK-STAT pathway and the somatic, activating mutation V617F in the pseudokinase domain of JAK2 has been reported in over 90% of patients with polycythemia vera, 40-70% of essential thrombocytemia and 40-60% of primary myelofibrosis. JAK2 mutations have not been described in papillary thyroid carcinomas. Moreover, this variant has high prevalence in the East Asian population, and thus is predicted be a germline variant. Clinical correlation with other laboratory findings is recommended.
The STK11 is a tumor suppressor gene located on chromosome 19p13.3. The encoded protein has serine--threonine kinase activity. Functionally, STK11 regulates cellular energy metabolism and cell polarity by activating AMP-activated protein kinase (AMPK) and other members of the AMPK family. Germline mutations in the STK11 gene are responsible for Peutz--Jeghers syndrome, an autosomal dominant disorder with variable clinical phenotype and increased risk of some cancers. Somatic mutations of STK11 gene are reported in several tumors including ~5% of cutaneous squamous cell carcinomas. According to Clinvar, this variant (c.597+1G>A) is considered to be oncogenic (https://preview.ncbi.nlm.nih.gov/clinvar/variation/265451/). This variant has been described as a germline variant that results in exon 4 skipping in a family with Peutz--Jeghers syndrome. Clinical correlation is recommended.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Codon I1307 lies within a regulatory region of the APC protein mediated by ubiquitination. Germline APC I1307K is associated with increased colorectal cancer risk by making the gene unstable and prone to acquire mutations during normal cell division. The germline APC I1307K gene mutation is most commonly found in people of Ashkenazi Jewish descent. Therefore, routine colorectal screening is very important in these individuals. One study showed that males had significantly increased I1307K carrier prevalence in lung, urologic, pancreatic, and skin cancers. APC somatic mutations are found 4% of lung adenocarcinomas. The I1307K has not been reported as a somatic mutation in lung adenocarcinomas to date. The prognostic and therapeutic implications of somatic APC mutations in lung adenocarcinomas remain to be fully elucidated. Correlation with other clinical and lab findings is recommended.
The protein encoded by the RB1 gene is a negative regulator of the cell cycle and was the first tumor suppressor gene identified. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Inactivation of RB1 and loss of RB1 tumor suppressor function has been identified in many early stage cancers. RB1 alterations are found in approximately 8% of non-small cell lung cancers. RB1 S576fs*34 results in early truncation of the RB1 protein and presumably loss of function. The predictive and prognostic significance of RB1 mutations in lung non-small cell carcinoma is undergoing further investigation. It has been suggested that patients with RB1-deficient tumors do not respond to cyclin-dependent kinase (CDK) inhibitors; however, the clinical implication of the loss of a single copy of RB1, as in this patient's case, remains to be fully elucidated. These results should be interpreted in the clinical context.
PTEN is a tumor suppressor gene, and loss of PTEN results in upregulation of the PI3K/ AKT pathway. Loss of PTEN is most commonly due to promoter hypermethylation, while homozygous deletion and nonsense mutations with loss of heterozygosity (LOH) may also occur. PTEN mutations may occur in multiple exons. Somatic mutations in PTEN have been found in 4--8% of non-small cell carcinomas (NSCLC) including adenocarcinomas and squamous cell carcinomas. In preclinical studies, PTEN loss is associated with decreased sensitivity of EGFR mutant lung tumors to EGFR TKIs. Clinical trials assessing the efficacy of PI3K inhibitors in PTEN loss are being explored. This particular variant is known to be oncogenic. It has also been reported as pathogenic/likely pathogenic germline variant according to ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/376032/).
NOTCH1 is a transmembrane receptor, which plays a role in cell fate determination, growth, and survival. Somatic alterations in NOTCH1 are very rare in thyroid carcinomas and are identified in less than 1% of cases. NOTCH1 L2457V does not lie within any known functional domains of the NOTCH1 protein. L2457V has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on protein function is unknown. The L2457V variant has been reported as a benign/likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/380420/). These results should be interpreted in the clinicopathologic context.
KIT, also known as proto-oncogene c-Kit or tyrosine-protein kinase Kit or CD117, is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of tissue types. Signaling through CD117 plays a role in cell survival, proliferation, and differentiation. Altered forms of this receptor may be associated with some types of cancers. Somatic mutations of KIT in lung adenocarcinoma are relatively rare, reported up to 3.3% of the cases. The predictive and prognostic significance of KIT mutations in lung adenocarcinomas needs further elucidation. According to ClinVar, the clinical significance of this particular variant C844Y is unknown (https://preview.ncbi.nlm.nih.gov/clinvar/variation/409781/). Results should be interpreted in conjunction with other laboratory and clinical findings.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR exon19 deletions, exon 21 L858R and Exon 18 mutations correlate strongly with sensitivity to specific EGFR inhibitors, and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M. Compound (dual) mutations in EGFR have been previously reported in lung adenocarcinoma and typically include a strong activating mutation combined with a weaker activating mutation. These cases appear to respond well to the EGFR targeted therapies. Mutations at E709 in exon 18 often occur together with other mutations in EGFR. This particular complex deletion insertion variant results in both the E709V and G719C in the protein, as well as a K713R variant, which also has been reported previously.
PTEN is a tumor suppressor gene, and loss of PTEN results in upregulation of the PI3K/ AKT pathway. Loss of PTEN is most commonly due to promoter hypermethylation, while homozygous deletion and nonsense mutations with loss of heterozygosity (LOH) may also occur. PTEN mutations may occur in multiple exons. Somatic mutations in PTEN have been found in 4--8% of non-small cell carcinomas (NSCLC) including adenocarcinomas and squamous cell carcinomas. This particular variant is likely to be oncogenic. In preclinical studies, PTEN loss is associated with decreased sensitivity of EGFR mutant lung tumors to EGFR TKIs. Clinical trials assessing the efficacy of PI3K inhibitors in PTEN loss are being explored.
The cytoplasmic b-catenin protein is implicated as a cell-cell adhesion regulator coupled with cadherin and is considered as a member in the wingless/Wnt signal transduction pathway. Mutations in CTNNB1, the gene encoding b-catenin, tend to impact or even eliminate APC-dependent serine and threonine phosphorylation sites in exon 3, resulting in oncogenic stabilization of the protein. Mutations in the b-catenin gene are uncommon in NSCLC occurring in about 1-4% of the cases. CTNNB1 S37C is a gain of function mutation, has been described in 0.3% of non-small cell lung carcinomas and is likely oncogenic. However, its prognostic and therapeutic significance remains to be fully elucidated.
Colorectal cancers (CRCs) frequently harbor somatic mutations in the pathway members SMAD4. The prevalence of SMAD4, SMAD2, and SMAD3 mutations in sporadic CRCs was 8.6% (64 of 744), 3.4% (25 of 744), and 4.3% (32 of 744), respectively. Somatic SMAD4 mutations have been reported to be more common in advanced stages of CRCs and LOH at the SMAD4 locus has been associated with poor prognosis. SMAD4 mutations were associated with mucinous histology. SMAD4 P356L has been identified in tumors. Although it has not been biochemically characterized, it is a statistically significant hotspot and is predicted to be oncogenic.
ERBB4 is a member of the EGFR subfamily of receptor tyrosine kinases. Approximately 5.4% of non-small cell lung cancers harbor ERBB4 missense mutations (COSMIC). In addition, 5.2% of adenocarcinomas have mutations in the ERBB4 gene that encode an amino acid change in the receptor. Activating, potentially oncogenic ERBB4 mutations (in particular Y285C, D595V, D931Y, and K935I) have been identified. However, the functional effects of lung cancer associated ERBB4 mutations is largely unknown. ERBB4 P920H variant has been seen in one case of squamous cell carcinoma of the head and neck (cancer.sanger.ac.uk). However, further studies are warranted to assess the potential prognostic and therapeutic significance of this and other variants of ERBB4.
CDKN2A gene functions as an important tumor suppressor in various human malignancies including colorectal cancer, and its activation prevents carcinogenesis via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Somatic mutations of CDKN2A are present in various tumor types but have not been well characterized in colorectal cancer. However, epigenetic silencing of CDKN2A by hypermethylation has been reported to be a possible predictive factor of poor prognosis in patients with colorectal cancer. CDKN2A R128W is predicted to confer a loss of function to the CDKN2A protein, as demonstrated by a loss of Sp1 binding. CDKN2A R128Q has been shown to be associated with dysplasia in the setting of Barrett's esophagus. However, its prognostic and therapeutic significance in colorectal carcinomas remains to be fully elucidated.
The PTPN11gene encodes SHP-2, a widely expressed cytoplasmic protein tyrosine phosphatase. SHP-2 is essential for activation of the RAS/MAPK signaling cascade. Most mutations are gain-of-function and result in prolonged ligand-dependent activation of the RAS/MAPK cascade. Germ-line PTPN11 mutations cause Noonan syndrome, a developmental disorder characterized by an increased risk of malignancies. Activating somatic mutations in PTPN11 have been documented in certain hematologic malignancies but they are infrequent in solid tumors. Approximately 2% of colonic adenocarcinomas harbor somatic mutations in the PTPN11 gene. The E76K variant of PTPN11 has been found to be oncogenic in gliomas, but their prognostic and therapeutic significance in colonic adenocarcinomas remains to be fully elucidated (https://oncokb.org/#/gene/PTPN11/alteration/E76K).
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR inhibitors (eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. EGFR Exon 19 deletions, EGFR Exon 21 L858R and EGFR Exon 18 G719 mutations correlate strongly with sensitivity to specific EGFR inhibitors and the response rate to therapy with TKIs has been reported to be up to 80% in such cases. The T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. However, third generation TKI (eg, osimertinib) can specifically target T790M. EGFR R108K (C.323G>A) is a rare missense mutation in Exon 3. In a study of 1006 lung carcinomas, R108K mutation was found concomitantly with other EGFR mutations - most notably p.L858R (Illei et.al). However, its prognostic and therapeutic significance remains to be fully elucidated.
The p.T1010I mutation, in the cytoplasmic juxtamembrane domain of MET has been shown to increase growth factor independent proliferation and motility in vitro in tumor cell lines in some studies. Approximately 2% of adenocarcinomas of the stomach harbor MET mutations. The utility of MET pathway inhibitors also continues to be explored. This variant has also been reported as a germline variant present in less than 1% of the general population. Its role in tumor development and progression continues to be studied. Due to conflicting reports of pathogenicity, this variant best characterized as a variant of uncertain significance (VUS) https://www.ncbi.nlm.nih.gov/clinvar/variation/41624/.
CTNNB1 encodes the protein b-catenin, a transcriptional activator involved in the WNT signaling pathway. Somatic gain-of-function mutations in CTNNB1 result in aberrant accumulation of the b-catenin protein and are prevalent in a wide range of solid tumors, including endometrial carcinoma, ovarian carcinoma, hepatocellular carcinoma, and colorectal carcinoma, among others. Genetic alterations in CTNNB1 have been identified in 4% of non-small cell lung cancers. The CTNNB1 S437F mutation has been reported as pathogenic in lung adenocarcinoma, but no real progress has been made in targeting oncogenic mutant forms of CTNNB1 in lung cancer. However, CTNNB1 mutation-positive cancers are presumed to be resistant to pharmacologic inhibition of upstream components of the WNT pathway, instead requiring direct inhibition of b-catenin function. In one study pharmacological inhibition of b-catenin suppressed EGFR-L858R/T790M mutated lung tumor and genetic deletion of the b-catenin gene dramatically reduced lung tumor formation in transgenic mice, suggesting that b-catenin plays an essential role in lung tumorigenesis and that targeting the b-catenin pathway may provide novel strategies to prevent lung cancer development or overcome resistance to EGFR TKIs. These results should be interpreted in the clinical context.
The Von Hippel-Lindau (vHL) gene may be altered as a somatic (acquired) alteration and/or as a germline alteration associated with a rare autosomal dominant inherited cancer syndrome predisposing to a variety of malignant and benign tumors including clear cell renal cell carcinoma (ccRCC). The protein encoded by this gene is involved in the ubiquitination and degradation of hypoxia-inducible-factor (HIF), which is a transcription factor that plays a central role in the regulation of gene expression by oxygen. The VHL C162Y mutation has not been functionally or clinically validated. However, VHL C162F is known to be oncogenic, and therefore VHL C162Y is considered likely oncogenic. According to ClinVar, VHLC162F is also reported as a pathogenic germline variant (https://preview.ncbi.nlm.nih.gov/clinvar/variation/223225/). These results should be interpreted in the clinicopathologic context and appropriate germline genetic workup may be considered if clinically indicated.
PTEN is a tumor suppressor gene, and loss of PTEN results in upregulation of the PI3K/ AKT pathway. Loss of PTEN is most commonly due to promoter hypermethylation, while homozygous deletion and nonsense mutations with loss of heterozygosity (LOH) may also occur. PTEN mutations may occur in multiple exons. Somatic mutations in PTEN have been found in 4--8% of non-small cell carcinomas (NSCLC) including adenocarcinomas and squamous cell carcinomas. In preclinical studies, PTEN loss is associated with decreased sensitivity of EGFR mutant lung tumors to EGFR TKIs. Clinical trials assessing the efficacy of PI3K inhibitors in PTEN loss are being explored. This particular variant is known to be oncogenic.
The catalytic subunit (p110a) of phosphatidylinositol-3-kinase (PI3K) is encoded by the PIK3CA gene and acts to activate several signaling cascades, including the well-characterized AKT-mTOR pathway that promotes cell survival, proliferation, growth and motility. PIK3CA is among the most commonly mutated genes in cancer and aberrant activation of PI3K is a transforming event. Somatic mutations in PIK3CA are seen in approximately 2% of papillary thyroid carcinoma, poorly differentiated carcinoma, anaplastic carcinoma. Somatic mutations of PIK3CA have been described particularly in advanced and dedifferentiating thyroid tumors. Their prevalence varies from 16 to 23% in anaplastic thyroid carcinomas. They are less frequent in papillary and follicular thyroid carcinomas and the prevalence in medullary thyroid carcinomas remains unknown. Although inhibitors of the PI3K/AKT/mTOR pathway have shown efficacy against thyroid cancer in pre-clinical models, their success in clinical trials remains to be determined.
Somatic mutations in BRAF have been found in 1-4% of all NSCLC most of which are adenocarcinomas and may be a potential therapeutic target in some settings. The BRAF V590I variant lies within the protein kinase domain of the Braf protein, has not been biochemically characterized, but results in similar cell proliferation and viability levels to wild-type Braf in culture (PMID: 29533785), and therefore is predicted to have no effect on Braf protein function, but its oncogenic potential has not been characterized. Clinical correlation is recommended.
MET is a member of the receptor tyrosine kinase and proto-oncogene playing a major role in tumor development and metastasis. Nonsynonymous mutations in the MET gene have been rarely described in sarcomas (<2%). The N375K variant has been reported as a somatic variant in two cases of NSCLC. It has been also reported in a single family with familial EGFR-mutant lung adenocarcinoma. This variant lies in the non-kinase domain of the protein. Further functional studies showed this mutation reduced the binding affinity of MET for its ligand, hepatocyte growth factor (HGF), damaging subsequent cellular processes including proliferation, motility and tumorigenicity. In ClinVar it is reported as a germline variant of unknown significance (https://preview.ncbi.nlm.nih.gov/clinvar/variation/572621/). The activity of MET inhibitors in tumors with non-kinase domain MET mutations is not yet known. The clinical significance of this mutation in this tumor is uncertain. Clinical correlation is recommended.
Mutations of the ESR1 gene have been increasingly recognized as an important mechanism of endocrine therapy resistance, with a prevalence that ranges from 11 to 39%. The majority of these mutations are located within the ligand-binding domain, especially codon 537 and 538, and result in an estrogen-independent constitutive activation of the ER and, therefore, resistance to estrogen deprivation therapy such as aromatase inhibition.
This MPL variant has been previously reported in the COSMIC database (COSM28997) and has been reported to be an activating mutation (PubMed ID: 26423830, Milosevic Feenstra et al., Blood 2016).
H3F3A K28M mutation (more commonly referred to as K27M) is a diagnostic parameter for the 2016 WHO-recognized entity, "Diffuse Midline Glioma H3 K27M-mutant", an astrocytic diffusely infiltrating tumor arising in the midline, typically within the brainstem, but also sometimes arising in the diencephalon or spinal cord. These tumors have a poor prognosis. The H3K27M alteration, which is characteristically heterozygous, leads to a decrease in overall H3K27me3 levels through dysregulation of the polycomb repressive complex 2 (PRC2), and a concurrent increase in H3K27 acetylation levels. Research is ongoing in an effort to develop ways to exploit this characteristic molecular alteration through targeted strategies.
The MPL p.S505N mutation is a recurrent mutation in some myeloproliferative and/or myeloproliferative/myelodysplastic disorders. It has also been reported in familial essential thrombocythemia. Biochemical studies of this variant have shown that it leads to moderate activation of downstream pathways including MEK-1/-2 and STAT5, which represent potentially targetable pathways.
SMARCB1 is a member of the SWI/SNF chromatin remodeling complex and regulates transcription of several genes involved in cell proliferation. SMARCB1 mutations are rare in colorectal adenocarcinomas and are reported in only about 1% of cases. Although not biochemically assessed, SMARCB1 R377H has been identified as a statistically significant hotspot and is predicted to be oncogenic. The clinicopathologic significance of SMARCB1 variants in colorectal cancer remains to be further elucidated.
Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) gene are present in approximately 80% of the lung adenocarcinomas that respond to first and second generation EGFR tyrosine kinase inhibitors (TKIs, eg, gefitinib, erlotinib and afatinib). Two types of mutations account for approximately 80-90% of all EGFR mutations: short in-frame deletions in Exon 19 and a point mutation in exon 21 at codon 858 (L858R). Other less common mutations in exons 18, 20, and 21 are found in 10-20% of EGFR-mutated cases. Exon 20 mutations are more commonly associated with resistance to tyrosine kinase inhibitors (TKIs), but may respond to third generation TKI (eg, osimertinib). This EGFR variant (G796S) lies within the tyrosine kinase domain and has been reported in rare cases of lung adenocarcinomas, squamous cell carcinoma of head and neck and prostate adenocarcinoma. In silico studies suggest G796S mutation may confer resistance to TKIs. However, additional studies are needed to further elucidate the oncogenicity of the mutation and therapeutic implications of this rare variant.
IDH1 is an enzyme localized to the cytoplasm and peroxisomes and involved in citrate metabolism. IDH-mutant tumors have aberrant production and accumulation of the oncometabolite 2-hydroxyglutarate (2-HG), which may play a pivotal oncogenic role in several malignancies including AML, central nervous system and biliary tract. Strikingly, IDH1 mutations were rarely detected in the other solid tumor types. While IDH1 mutations have been reported in 1-2% of lung adenocarcinomas, the clinical significance of this mutation with regards to response to anti-IDH1 therapy in lung cancer is unknown. This specific IDH1 p.PR119Q has been identified in numerous reports, but it has not been biochemically characterized and its effect on protein function is unknown. Results should be interpreted in conjunction with other laboratory and clinical findings.
CDKN2A gene functions as an important tumour suppressor in various human malignancies and somatic mutations in this gene are present in various tumor types, including, lung adenocarcinoma, squamous cell carcinoma of the larynx, clear cell sarcoma, head and neck cancer, melanoma and esophageal cancer, among other cancer types. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. This particular variant G67C is considered to be likely pathogenic based on the known pathogenicity of G67R/S. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types.
Somatic mutations of CDKN2A are present in various tumor types, including, squamous cell carcinoma of the larynx, clear cell sarcoma, head and neck cancer, esophageal cancer and melanoma. Germline aberrations in the CDKN2A gene are also observed in some melanoma-prone families, representing high penetrance mutations. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types. Correlation with clinical findings and genetic counseling may be helpful if there is clinical concern for an inherited cancer syndrome.
Somatic mutations of CDKN2A are present in various tumor types, including, squamous cell carcinoma of the lung, clear cell sarcoma, head and neck cancer, melanoma and esophageal cancer. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. The D84V mutant is predicted to confer loss of function to the CDKN2A protein as demonstrated by an inability to bind and inhibit the cyclin-dependent kinases CDK4 and CDK6. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types.
Smoothened (SMO) is a co-receptor involved in the Hedgehog (Hh) signaling. Constitutive or aberrant activation of the Hh pathway leading to tumorigenesis is seen in many cancers with SMO activating mutations identified in basal cell carcinoma and medulloblastoma. Several Hh signaling pathway inhibitors, such as vismodegib and sonidegib, have been recently developed for cancer treatment. Germline or somatic SMO mutations have not been previously characterized in NSCLC; however, in a recent report a germline SMO P641A mutation in a patient with refractory NSCLC responded to vismodegib therapy for several months. The functional effect of SMO V404M is conflicting as it demonstrated activity similar to the normal protein in culture in one study, but resulted in near complete loss of Hh pathway signaling in another study, and therefore, its effect on SMO protein function is unknown. Clinical correlation is recommended.
The Von Hippel-Lindau (vHL) gene encodes a protein that is involved in the ubiquitination and degradation of hypoxia-inducible-factor (HIF), which is a transcription factor that plays a central role in the regulation of gene expression by oxygen. The VHL gene may be altered as a somatic (acquired) alteration and/or as a germline alteration associated with a rare autosomal dominant inherited cancer syndrome predisposing to a variety of malignant and benign tumors including clear cell renal cell carcinoma (ccRCC). Alterations in VHL have been reported in less than 1% of lung adenocarcinomas. The VHL p.G144* has been reported in multiple renal cell carcinomas as a somatic alteration. According to ClinVar, the VHL p.G144* is also reported as a pathogenic germline variant (https://www.ncbi.nlm.nih.gov/clinvar/variation/223208/). These results should be interpreted in the clinicopathologic context and appropriate germline genetic workup may be considered if clinically indicated.
PTEN is a tumor suppressor gene, and loss of PTEN results in upregulation of the PI3K/ AKT pathway. Loss of PTEN is most commonly due to promoter hypermethylation, while homozygous deletion and nonsense mutations with loss of heterozygosity (LOH) may also occur. PTEN mutations may occur in multiple exons. Somatic mutations in PTEN have been found in 4-8% of non-small cell carcinomas (NSCLC) including adenocarcinomas and squamous cell carcinomas. In preclinical studies, PTEN loss is associated with decreased sensitivity of EGFR mutant lung tumors to EGFR TKIs. Clinical trials assessing the efficacy of PI3K inhibitors in PTEN loss are being explored. The PTENI101T has been observed in a variety of cancer types, most frequently gliomas, and has been predicted to be pathogenic. However, one study identified the PTEN I101T variant in 1 out of 172 patients with germline PTEN mutations.
The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Somatic mutations in APC have been reported in 4% of lung adenocarcinomas, the prognostic and therapeutic implications of which remain to be fully elucidated. APC K1454E lies within the beta-catenin binding and down-regulation region of the Apc protein. K1454E suppresses beta-catenin mediated transcription at a level similar to wild-type Apc in a cell culture assay and therefore, is predicted to have no effect on Apc protein function. This variant has also been reported as a germline variant in prior studies and reported in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/RCV000200964/) as likely benign.
MET is a receptor tyrosine kinase that has been shown to frequently be altered (mutation or amplification) in various cancers, leading to overexpression. The p.T1010I mutation, in the cytoplasmic juxtamembrane domain of MET has been shown to increase growth factor independent proliferation and motility in vitro in tumor cell lines in some studies. However, the functional effect of T1010I is conflicting, as it has been reported both to have phosphorylation level and transforming capacity similar to wild-type Met protein (PMID: 20670955) This variant has also been reported as a germline variant present in less than 1% of the general population. Its role in tumor development and progression continues to be studied. Due to conflicting reports of pathogenicity, this variant best characterized as a variant of uncertain significance (VUS) (https://www.ncbi.nlm.nih.gov/clinvar/variation/41624/).
Somatic mutations in BRAF have been found in up to 10% of all NSCLC, more common in adenocarcinomas. D594 is a highly conserved residue within the kinase domain of BRAF and mutation of this residue appears to result in kinase inactivation. In vitro study has shown that kinase-dead BRAF forms a constitutive complex with CRAF in the presence of activated RAS leading to MEK and ERK signaling.While clinical trials targeting BRAF-mutant NSCLC have mostly focused on patients with V600E-mutant disease, in vitro studies suggests potential sensitivity to targeted agents in cell lines with inactivating BRAF non-V600 mutations. However, established clinical activity of targeted BRAF and MEK inhibition in patients with these mutations has yet to be fully elucidated and further study is warranted. Clinical correlation is recommended.