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.

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

The D594E mutation in BRAF is believed to result in inactivation of BRAF and, therefore, BRAF inhibitors are not likely to be effective.

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.

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

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.

The MLH1 V384D polymorphism has been associated with cancer risk in some tumor types. In addition, according to one report, MLH1 V384D polymorphism has been reported to be associated with primary resistance to EGFR-TKIs in patients with EGFR L858R-positive lung adenocarcinoma and may potentially be a novel biomarker to guide treatment decisions for those patients. The effect of this MLH1 polymorphism when present with other EGFR-TKI sensitizing mutations such as Exon 19 deletions in EGFR remains to be clarified. Some studies have shown that patients carrying the MLH1 V384D variant have an increased risk of the development of microsatellite-instable as well as -stable colorectal cancer. This variant has an allele frequency of 4% in the East Asian population. Of note, this variant is reported as a benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/41632/). Clinical correlation is recommended.

NRAS mutations occur in approximately 1--6% of colorectal cancers. Several studies have shown that patients with NRAS-mutated tumors are less likely to respond to cetuximab or panitumumab, but this may not have an effect on PFS or overall survival.

Somatic mutations in 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

FGFR1 activating mutations may be associated with response to the multitargeted tyrosine kinase inhibitor pazopanib.

FGFR1 amplification may be associated with sensitivity to the multitargeted tyrosine kinase inhibitor pazopanib in some tumor types.

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

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.

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.

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.

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.

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.

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.

The epidermal growth factor receptor (EGFR) is a cell surface receptor belonging to the ErbB family tyrosine kinase receptors. EGFR is involved in cell growth control through its role in the two main intracellular pathways, the mitogen-activated protein kinase (MAPK) pathway and the phosphatidylinositol 3-kinase- (PI3K-) protein kinase B (AKT) pathway. The over-expression or mutation of EGFR may be responsible for the constitutive activation of these pathways. In colorectal cancer, EGFR has been found to be frequently over expressed, and may be associated with tumor stage and prognosis. Somatic EGFR mutations are infrequent in colorectal cancers. The frequency of EGFR mutations in colorectal cancer varies from 0.34 to 3.3% in Western population, and from 12% to 22.4% in Asians. In a subset of patients with EGFR mutations in colorectal cancer, the addition of anti-EGFR monoclonal antibodies to the conventional chemotherapeutic regimens may expand response rates and increase progression-free survival. EGFR V765M lies within the protein kinase domain of the protein. In lung cancer, the V765M has been reported as a sensitizing mutation to EGFR tyrosine kinase inhibitors. The correlation of EGFR gene mutations with clinicopathologic characteristics in colorectal cancers continues to be explored.

Somatic mutations in 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.

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.

NOTCH1 is a transmembrane receptor, which plays a role in cell fate determination, growth, and survival. Somatic activating mutations are common in T-cell lymphoblastic leukemia/lymphoma. Somatic alterations in NOTCH1 are very rare in colorectal adenocarcinoma and are identified in less than 1% of cases. NOTCH1 L2457V does not lie within any known functional domains of the NOTCH1 protein. L2457V has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on protein function is unknown. The L2457V variant has been reported as a benign/likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/380420/). These results should be interpreted in the clinicopathologic context.

Somatic APC mutations are common events in colorectal adenocarcinomas, reported in up to 76% of the cases. Loss of normal APC function is known to be an early event in both familial and sporadic colon cancer pathogenesis, occurring at the pre-adenoma stage. APC mutations do not appear to significantly affect the prognosis of colorectal cancer patients. While there are a number of small molecule inhibitors in development that target the Wnt pathway, there is currently no matched targeted therapy available for colorectal cancer patients harboring an APC mutation. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Codon I1307 lies within a regulatory region of the APC protein mediated by ubiquitination. APC I1307K is associated with increased colorectal cancer risk by making the gene unstable and prone to acquire mutations during normal cell division. The germline APC I1307K gene mutation is most commonly found in people of Ashkenazi Jewish descent. Therefore, routine colorectal screening is very important in these individuals. Correlation with other clinical and lab findings is recommended.

FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. FBXW7 R505C lies within the WD4 repeat region and confers a loss of FBXW7-substrate interaction and impairs substrate degradation by FBXW7, resulting in sustained NICD and MYC expression. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin; A single study has reported only limited activity in phase I trials using mTOR inhibitors in patients with advanced cancers including colorectal cancer. The clinical utility remains unknown.

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.

FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. Due to the disruption of the WD repeat domain, the FBXW7 R393* truncating mutation is predicted to lead to a loss of FBXW7 protein function. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin; however, the clinical utility remains unknown. A single study has reported only limited activity in phase I trials using mTOR inhibitors in patient with advanced cancers including colorectal cancer.

Vemurafenib Dabrafenib Dabrafenib + Trametinib Vemurafenib + Cobimetinib Vemurafenib + Panitumumab Encorafenib + Binimetinib + Cetuximab Radiation + Trametinib + Fluorouracil

BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Approximately 8--15% of colorectal cancer (CRC) harbors BRAF mutations. BRAF G469V mutation in exon 11 is infrequent in CRC and occurs within the kinase domain. The presence of BRAF mutation is significantly associated with right-sided colon cancers and is associated with decreased overall survival. BRAF mutation in a microsatellite unstable colorectal carcinoma indicates that the tumor is probably sporadic and not associated with Lynch syndrome (HNPCC). However, if a BRAF mutation is not detected, the tumor may either be sporadic or Lynch syndrome associated. Detection of BRAF mutations may also be useful in determining patient eligibility for anti-EGFR treatment. Some studies have reported that patients with metastatic CRC (mCRC) that harbor BRAF mutations do not respond to anti-EGFR antibody agents (cetuximab or panitumumab) in the chemotherapy-refractory setting. Results should be interpreted in conjunction with other laboratory and clinical findings.

KDR encodes the protein VEGF2, a receptor tyrosine kinase that regulates angiogenesis and vascular development. While KDR mutations are rare, amplification or protein overexpression have been reported in small proportion of a variety of solid tumors. KDR P263T has not been characterized and the effect on protein function is unknown. These results should be interpreted in the clinical context.

Colorectal cancers (CRCs) frequently harbor somatic mutations in the pathway members SMAD4. The prevalence of SMAD4, SMAD2, and SMAD3 mutations in sporadic CRCs was 8.6% (64 of 744), 3.4% (25 of 744), and 4.3% (32 of 744), respectively. SMAD4 R361C lies at a hotspot residue within MH2 domain and has displayed reduced SMAD4 transactivating activity in cell assays. Somatic SMAD4 mutations have been reported to be more common in advanced stages of CRCs. Studies of loss of function somatic mutations and studies of loss of heterozygosity (LOH) at the SMAD4 locus have shown an association with poor prognosis. SMAD4 mutations were also associated with mucinous histology. There are ongoing clinical trials for colorectal tumors harboring SMAD4 alterations.

BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway. BRAF G466V is a missense mutation which impairs BRAF kinase activity but paradoxically activates MEK and ERK through transactivation of c-RAF. This variant is associated with decreased cell proliferation and cell viability as compared to wild-type BRAF. This variant is a rare BRAF mutation and accounts for < 1% of BRAF mutations in colorectal adenocarcinoma. A single preclinical study of BRAF G466V in colon cancer demonstrated sensitivity to anti-EGFR tyrosine kinase therapy (cetuximab) and a MEK inhibitor (trametinib), however, there was no benefit seen with the RAF inhibitor vermurafinib. The clinicopathologic significance of BRAF G466V remains to be fully elucidated.

SMARCB1 is a member of the SWI/SNF chromatin remodeling complex and regulates transcription of several genes involved in cell proliferation. SMARCB1 R374Q does not lie within any known functional domains of the SMARCB1 protein. R374Q has been identified in sequencing studies, but has not been biochemically characterized and therefore, its effect on protein function is unknown. SMARCB1 mutations are rare in colorectal adenocarcinomas and are reported in only about 1% of cases. The clinicopathologic significance of SMARCB1 variants in colorectal cancer remains to be further elucidated.

This gene encodes the catalytic subunit of DNA polymerase epsilon. The enzyme is involved in DNA repair and chromosomal DNA replication. Mutations in this gene have been associated with colorectal and endometrial cancer. P285R is the most common recurrent mutation of POLE in those types of cancers. Somatic POLE mutation is associated with approximately 3% of sporadic microsatellite-stable (MSS) but hypermutated CRCs.

PTEN is an obligate haplo-insufficient tumor suppressor gene and is commonly mutated in a large number of cancers. It negatively regulates intracellular levels of phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Approximately 20-30% of colorectal carcinomas involve biallelic inactivation of PTEN through a combination of genetic and epigenetic mechanisms. The R15I missense mutation falls within the PIP2 binding motif in the phosphatase domain of PTEN, which involves residues 6-15. PTEN R15I has been show to result in loss of phosphatase activity in vitro. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.

KDR encodes the protein VEGF2, a receptor tyrosine kinase that regulates angiogenesis and vascular development. While KDR mutations are rare, amplification or protein overexpression have been reported in small proportion of a variety of solid tumors. It is unclear if KDR mutation plays a role in colorectal carcinoma pathogenesis; however, it may have a role in clinical outcome prediction and therapeutic response. For example, increased expression of VEGFA, FLT1, and KDR in colorectal carcinoma is associated with a poor prognosis and lack of response to bevacizumab therapy. Although the functional consequence of KDR K270N has not been characterized, it has been reported previously as a somatic variant in in colorectal carcinomas. These results should be interpreted in the clinical context. Most therapies blocking KDR signaling target the angiogenesis pathway in general, such as bevacizumab, an antibody that targets VEGF-A.

KIT (CD117) is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of human tissues. Gain-of-function mutations of the KIT gene have been identified that produce ligand-independent activation of KIT and cell proliferation. KIT receptor and its ligand have been demonstrated in human colon cancer cell lines. Some studies have shown high frequency of KIT overexpression in stage II colon cancer patients (59.3%) with significant correlation between KIT overexpression and reduced disease free survival. However, other studies failed to demonstrate KIT expression in a significant number of colorectal cancers suggesting that KIT kinase activation is not a prominent pathogenetic feature of colorectal cancers. Role of KIT continues to be studied in colon cancers. KIT K807N missense mutation is known to be oncogenic. Several tyrosine kinase inhibitors against KIT are available, mainly for gastrointestinal stromal tumors and melanoma. The role of these targeted therapies in colorectal carcinomas need to be further elucidated.

Somatic mutations in PIK3CA have been found in 10--30% of colorectal cancers. KRAS, NRAS, BRAF and PIK3CA and non-functional PTEN predict resistance to anti-EGFR therapies in metastatic colorectal cancer. Recent 'molecular pathological epidemiology' (MPE) research has shown that aspirin use may be associated with better prognosis and clinical outcome in PIK3CA-mutated colorectal carcinoma, suggesting somatic PIK3CA mutation may be a molecular biomarker that predicts response to aspirin therapy. The R88Q mutation falls within the ABD domain of the p110a catalytic subunit and has been shown to result in gain-of-function in vitro. PIK3CA may be a target of directed therapy in some clinical settings.

FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes and is inactivated by mutation in various cancers, most frequently in endometrial and colorectal cancers. Substrates of FBXW7 include the proteins c-MYC, mTOR, NOTCH1, cyclin-E, and JUN, which are instrumental in the regulation of cell division, differentiation and growth, and which are often inappropriately activated in cancer. Inactivation of FBXW7 by mutation or copy number loss results in aberrant accumulation of the above oncoproteins, which subsequently contributes to malignant transformation. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. Most mutations in FBXW7 are point mutations that disrupt substrate binding, while <10% are small deletions or insertions. FBXW7 is altered in 17% of colorectal adenocarcinomas. The FBXW7 R465H variant is considered to be likely oncogenic. Preclinical data have suggested that inactivating mutations of FBXW7 could predict sensitivity to the mTOR inhibitor rapamycin. A single study has reported only limited activity in phase I trials using mTOR inhibitors in patients with advanced cancers including colorectal cancer. The clinical utility remains unknown.

The proto-oncogene KIT encodes a type 3 transmembrane receptor tyrosine kinase. c-kit (CD117) is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of human tissues. Gain-of-function mutations of the c-kit gene have been identified that produce ligand-independent activation of c-kit and cell proliferation. Some of these mutations appear causative in the pathogenesis of adult mastocytosis and most gastrointestinal stromal tumors (GISTs). Activating KIT mutations occur in 80 - 90% of GISTs and several small molecule tyrosine kinase inhibitors (TKIs) targeting KIT that have been approved by the US Food and Drug Administration with the efficacy of each TKI strongly depending on the location of the activating KIT mutation. c-kit receptor and its ligand have been demonstrated in human colon cancer cell lines. Some studies have shown high frequency of c-Kit overexpression in stage II colon cancer patients (59.3%) with significant correlation between c-Kit overexpression and reduced disease free survival. However, other studies failed to demonstrate c-kit expression in a significant number of colorectal cancers suggesting that c-kit kinase activation is not a prominent pathogenetic feature of colorectal cancers. The role of c-Kit continues to be studied in colon cancers. The KIT D52N mutation likely represent an oncogenic gain of function mutation.

KIT, also known as proto-oncogene c-Kit or tyrosine-protein kinase Kit or CD117, is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of tissue types. Signaling through CD117 plays a role in cell survival, proliferation, and differentiation. Altered forms of this receptor may be associated with many types of cancers including hematopoietic malignancies, gastrointestinal stromal tumors, and various carcinomas and sarcomas. KIT G565V lies within the cytoplasmic domain of the Kit protein; this variant has been documented in the scientific literature (in melanoma). While its effect on Kit protein function is unknown, it is reported in ClinVar as likely benign germline variant (https://preview.ncbi.nlm.nih.gov/clinvar/variation/41600/).

Colorectal cancers (CRCs) frequently harbor somatic mutations in the pathway members SMAD4. The prevalence of SMAD4, SMAD2, and SMAD3 mutations in sporadic CRCs was 8.6% (64 of 744), 3.4% (25 of 744), and 4.3% (32 of 744), respectively. Somatic SMAD4 mutations have been reported to be more common in advanced stages of CRCs and LOH at the SMAD4 locus has been associated with poor prognosis. SMAD4 mutations were associated with mucinous histology. SMAD4 P356L has been identified in tumors. Although it has not been biochemically characterized, it is a statistically significant hotspot and is predicted to be oncogenic.

CDKN2A gene functions as an important tumor suppressor in various human malignancies including colorectal cancer, and its activation prevents carcinogenesis via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Somatic mutations of CDKN2A are present in various tumor types but have not been well characterized in colorectal cancer. However, epigenetic silencing of CDKN2A by hypermethylation has been reported to be a possible predictive factor of poor prognosis in patients with colorectal cancer. CDKN2A R128W is predicted to confer a loss of function to the CDKN2A protein, as demonstrated by a loss of Sp1 binding. CDKN2A R128Q has been shown to be associated with dysplasia in the setting of Barrett's esophagus. However, its prognostic and therapeutic significance in colorectal carcinomas remains to be fully elucidated.

The PTPN11gene encodes SHP-2, a widely expressed cytoplasmic protein tyrosine phosphatase. SHP-2 is essential for activation of the RAS/MAPK signaling cascade. Most mutations are gain-of-function and result in prolonged ligand-dependent activation of the RAS/MAPK cascade. Germ-line PTPN11 mutations cause Noonan syndrome, a developmental disorder characterized by an increased risk of malignancies. Activating somatic mutations in PTPN11 have been documented in certain hematologic malignancies but they are infrequent in solid tumors. Approximately 2% of colonic adenocarcinomas harbor somatic mutations in the PTPN11 gene. The E76K variant of PTPN11 has been found to be oncogenic in gliomas, but their prognostic and therapeutic significance in colonic adenocarcinomas remains to be fully elucidated (https://oncokb.org/#/gene/PTPN11/alteration/E76K).

The Von Hippel-Lindau (vHL) gene may be altered as a somatic (acquired) alteration and/or as a germline alteration associated with a rare autosomal dominant inherited cancer syndrome predisposing to a variety of malignant and benign tumors including clear cell renal cell carcinoma (ccRCC). The protein encoded by this gene is involved in the ubiquitination and degradation of hypoxia-inducible-factor (HIF), which is a transcription factor that plays a central role in the regulation of gene expression by oxygen. The VHL C162Y mutation has not been functionally or clinically validated. However, VHL C162F is known to be oncogenic, and therefore VHL C162Y is considered likely oncogenic. According to ClinVar, VHLC162F is also reported as a pathogenic germline variant (https://preview.ncbi.nlm.nih.gov/clinvar/variation/223225/). These results should be interpreted in the clinicopathologic context and appropriate germline genetic workup may be considered if clinically indicated.

SMARCB1 is a member of the SWI/SNF chromatin remodeling complex and regulates transcription of several genes involved in cell proliferation. SMARCB1 mutations are rare in colorectal adenocarcinomas and are reported in only about 1% of cases. Although not biochemically assessed, SMARCB1 R377H has been identified as a statistically significant hotspot and is predicted to be oncogenic. The clinicopathologic significance of SMARCB1 variants in colorectal cancer remains to be further elucidated.

MET is a receptor tyrosine kinase that has been shown to frequently be altered (mutation or amplification) in various cancers, leading to overexpression. The p.T1010I mutation, in the cytoplasmic juxtamembrane domain of MET has been shown to increase growth factor independent proliferation and motility in vitro in tumor cell lines in some studies. However, the functional effect of T1010I is conflicting, as it has been reported both to have phosphorylation level and transforming capacity similar to wild-type Met protein (PMID: 20670955) This variant has also been reported as a germline variant present in less than 1% of the general population. Its role in tumor development and progression continues to be studied. Due to conflicting reports of pathogenicity, this variant best characterized as a variant of uncertain significance (VUS) (https://www.ncbi.nlm.nih.gov/clinvar/variation/41624/).