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.

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.

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

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.

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.

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.

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/).

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

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.

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.

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.

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.

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. 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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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 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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

In colorectal cancer, EGFR gene amplification is associated with sensitivity EGFR-targeted therapies, such as Erbitux and Vectibix.

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

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.

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.

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.

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.

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

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.

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.

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.

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.

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.