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.

This gene is a known cancer gene.

This gene is a known cancer gene.

This gene is a known cancer gene.

This gene is a known cancer gene.

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.

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.

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.

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.

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.

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.

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.