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/).

Somatic mutations of CDKN2A are present in various tumor types, including, squamous cell carcinoma of the lung, clear cell sarcoma, head and neck cancer, melanoma and esophageal cancer. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types.

It is unclear what effect the EGFR P753S varaints has on the EGFR protein. However the location of the variant in the splice site acceptor of Exon 19 may activate the kinase domain. The identification of the EGFR P735S mutation in the context of a dramatic response to cetuximab in a patient with cutaneous squamous cell carcinoma, indicates a new potential pairing of EGFR mutation and targeted therapy for patients with cSCC.

KRAS belongs to the RAS family of oncogenes. In lung, KRAS mutations are detected in approximately 20% to 25% of adenocarcinoma and less than 10% of squamous cell carcinoma which demonstrate a minor glandular component. KRAS mutations in NSCLC most often occur in codons 12 or 13 and with a lower frequency in codon 61. Mutations in KRAS are usually mutually exclusive with other oncogenic driver aberrations including EGFR, BRAF, HER2 mutations and ALK and ROS1 rearrangements. Contrary to most other oncogenic driver mutations, KRAS is more often found in smokers and is detected at lower frequency in East Asian patient cohorts. The prognostic as well as predictive role of KRAS mutations continues to be studied. Although various attempts inhibiting KRAS have been made, there is no established therapy specific for this large patient subpopulation. Recommend correlation with other clinical and lab findings.

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.

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.

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.

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.

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.

EGFR mutations have been reported in up to 5% of gastric cancers. The prognostic and predictive implications of EGFR mutations in gastric cancer have not been fully determined. Multiple clinical trials involving EGFR small molecule inhibitors and monoclonal antibodies are present, but limited and conflicting data preclude the therapeutic significance of EGFR mutations in gastric cancer. In NSCLC, an acquired T790M mutation in exon 20 is associated with resistance to some EGFR inhibitors. Third generation TKIs (e.g. osimertinib) have been shown to be effective in lung adenocarcinomas with the EGFR T790M mutation. A germline EGFR T790M mutation results in a rare lung cancer hereditary syndrome associated with increased risk in never-smokers. The presence of a germline EGFR T790M mutation also predicts for resistance to standard TKIs. The significance of EGFR T790M in gastric cancer should be considered in a relevant clinical context. Drug Resistance: Afatinib Erlotinib Gefitinib

The catalytic subunit (p110a) of phosphatidylinositol-3-kinase (PI3K) is encoded by the PIK3CA gene and acts to activate several signaling cascades, including the well-characterized AKT-mTOR pathway that promotes cell survival, proliferation, growth and motility. PIK3CA is among the most commonly mutated genes in cancer and aberrant activation of PI3K is a transforming event. Somatic mutations in PIK3CA have been found in 1--3% of NSCLC and genetic alteration in PIK3CA have been identified in 7% of lung adenocarcinomas. These mutations typically occur within specific hotspot regions. PIK3CA mutations activate the PI3K-PTEN-AKT pathway which is downstream from both the EGFR and the RAS-RAF-MAPK pathways. The somatic mutations found thus far in PIK3CA are oncogenic, and the majority of them are clustered within exon 9 and 20 (helical and kinase domains), with three hotspots (E542K, E545K, and H1047R/L). PIK3CA mutations have been reported in 8-21% and 20-33% of head/neck and anal squamous cell carcinoma, respectively. PIK3CA mutations, especially ones involving the helical domain, in these types of squamous cell carcinoma are highly associated with HPV. The predictive and prognostic significance of PIK3CA mutations in squamous cell carcinoma is unclear and needs further elucidation. Clinical trials targeting PI3K/Akt/mTor pathway inhibitors are available for patients with PIK3CA mutated tumors.

RAS is a family of small GTPases and acts as an oncogene. Point mutations in codons 12 and 13 of RAS gene increases its affinity for GTP and those in codon 61 inactivate its autocatalytic GTPase function, resulting in permanent RAS activation and stimulation of its downstream targets along the MAPK and PI3K/AKT signaling pathways. HRAS mutation has been reported in up to 5% and 9% of head/neck and vulvar squamous cell carcinoma, respectively. The predictive and prognostic significance of HRAS mutations in squamous cell carcinoma is unclear and needs further elucidation.

PTCH1 loss of function mutations are associated with Vismodegib sensitivity in basal cell carcinoma. However, the clinical significance in other tumor types is unknown.

FGFR2 mutation in a patient with oral squamous cell carcinoma was associated with response to the multitargeted tyrosine kinase inhibitor pazopanib.

FGFR1 amplification is associated with poor survival in patients with resected squamous cell lung cancer. FGRF1 amplification may be associated with sensitivity to the multitargeted tyrosine kinase inhibitor pazopanib.

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.

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.

This gene is a known cancer gene. ARID1A/BAF250A subunit of the SWI/SNF (BAF) chromatin remodeling complex has emerged as recurrently mutated in a broad array of tumor types and a potential tumor suppressor. There is evidence indicating that ARID1A-mutated cancers may be subjected to therapeutic intervention.

Somatic mutations in TP53 are frequent in human cancer. Germline TP53 mutations cause of Li-Fraumeni syndrome, which is associated with a range of early-onset cancers. The types and positions of TP53 mutations are diverse. TP53 mutations may be potential prognostic and predictive markers in some tumor types, as well as targets for pharmacological intervention in some clinical settings. The IARC TP53 Database (http://www-p53.iarc.fr/) is a useful resource which catalogues TP53 mutations found in cancer.

CDKN2A gene functions as an important tumor suppressor via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of RB and p53 pathways. CDKN2A alterations have been reported as frequent mutations in squamous cell carcinomas of different primary sites including the lung, head and neck, and skin. CDKN2A R80* results in a premature truncation and confers a loss of function to the CDKN2A protein as demonstrated by loss of CDK binding. CDKN2A truncating mutations, including R80*, have been described in approximately 4% of esophageal squamous cell carcinomas. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials. The clinical significance of the loss of one copy of CDKN2A remains to be fully elucidated in squamous cell carcinoma of the esophagus. These results should be interpreted in the clinicopathologic context.

CDKN2A gene functions as an important tumor suppressor via induction of cell growth arrest and senescence. Majority of the CDKN2A mutations result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of RB and p53 pathways. CDKN2A alterations have been reported as frequent mutations in squamous cell carcinomas of different primary sites including the lung, head and neck, and skin. CDKN2A R58* results in a premature truncation and confers a loss of function to the CDKN2A protein as demonstrated by loss of CDK binding. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials. The clinical significance of the loss of one copy of CDKN2A remains to be fully elucidated in squamous cell carcinoma of the bladder. These results should be interpreted in the clinicopathologic context.

BRAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Approximately 10% of cutaneous squamous cell carcinomas harbor somatic mutations in BRAF. The G469A mutation in exon 11 results in an amino acid substitution at position 469 in BRAF, which occurs in the highly conserved motif of the kinase domain. Most mutant BRAF proteins, such as G469A, have increased kinase activity and are transforming in vitro. Though BRAF mutations and targeted therapies have been have been studied in other solid tumors, the predicative and prognostic significant in cutaneous squamous cell carcinoma is unclear and needs to be further investigated.

FBXW7 is a tumor suppressor gene that is mutated in several tumors including colorectal, liver, bladder and ovarian cancers. It is also mutated in endometrial, esophageal, and head and neck squamous cancers. FBXW7 is a tumor suppressor gene responsible for the degradation of several proto-oncogenes. mTOR is one of the substrates of FBXW7-mediated protein degradation, and loss of function of FBXW7 increases the levels of total and activated mTOR. FBXW7 R505G lies within the WD repeat 4 of the FBXW7 protein. R505G has been identified in the scientific literature, but has not been biochemically characterized and therefore, its effect on FBXW7 protein function is unknown. Preclinical data suggest that FBXW7 mutations may sensitize cells to mTOR inhibitors, however, the response to mTOR inhibitors and the clinicopathologic effects of FBXW7 R505G remains to be further elucidated.

Proto-oncogene tyrosine-protein kinase receptor RET, activates the MAPK pathway for cell proliferation and the PI3K/AKT pathway for cell survival. Certain inherited mutations in the RET proto-oncogene predispose individuals to the multiple endocrine neoplasia type 2 (MEN 2) cancer syndromes including MEN 2A and 2B, and familial medullary thyroid carcinoma. Somatic mutations in RET are rare in squamous cell carcinoma of the lung and are found in 2-3% of cases. RET E623K lies within the extracellular domain of the RET protein, but has not been characterized and therefore its effect on RET protein function is unknown. RET E623K has been reported as a benign germline mutation in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/24906/). These results should be interpreted in the clinical context.

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.

FGFR3 amplification may be associated with response to the multitargeted tyrosine kinase inhibitor pazopanib.

PTEN is a lipid and protein phosphatase that negatively regulates the PI3K/AKT/mTOR pathway. Cancer-associated alterations in this gene often result in loss of PTEN protein and upregulation of the PI3K/AKT/mTOR pathway. PTEN mutations have been reported in ~2% of head and neck squamous cell carcinomas and 15% of anaplastic thyroid carcinomas. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome. This particular variant M134I has been reported as a likely pathogenic germline variant (ClinVar, https://preview.ncbi.nlm.nih.gov/clinvar/variation/428267/) and has also been reported as a somatic variant. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.

B-RAF is a member of the RAF-family of kinases which plays an important role in the RAS-RAF-MEK-ERK mitotic signaling pathway. Mutations of B-RAF have been described in <2% of head and neck squamous cell carcinomas. The hotspot for mutations in BRAF is at codon Val600 and the most common one is p.Val600Glu (V600E). Various B-RAF inhibitors have been FDA approved for cancer therapy in certain settings.

The STK11 is a tumor suppressor gene located on chromosome 19p13.3. The encoded protein has serine--threonine kinase activity. Functionally, STK11 regulates cellular energy metabolism and cell polarity by activating AMP-activated protein kinase (AMPK) and other members of the AMPK family. Germline mutations in the STK11 gene are responsible for Peutz--Jeghers syndrome, an autosomal dominant disorder with variable clinical phenotype and increased risk of some cancers. Somatic mutations of STK11 gene are reported in several tumors including ~5% of cutaneous squamous cell carcinomas. According to Clinvar, this variant (c.597+1G>A) is considered to be oncogenic (https://preview.ncbi.nlm.nih.gov/clinvar/variation/265451/). This variant has been described as a germline variant that results in exon 4 skipping in a family with Peutz--Jeghers syndrome. Clinical correlation is recommended.

The protein encoded by the RB1 gene is a negative regulator of the cell cycle and was the first tumor suppressor gene identified. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Inactivation of RB1 and loss of RB1 tumor suppressor function has been identified in many early stage cancers. RB1 alterations are found in approximately 8% of non-small cell lung cancers. RB1 S576fs*34 results in early truncation of the RB1 protein and presumably loss of function. The predictive and prognostic significance of RB1 mutations in lung non-small cell carcinoma is undergoing further investigation. It has been suggested that patients with RB1-deficient tumors do not respond to cyclin-dependent kinase (CDK) inhibitors; however, the clinical implication of the loss of a single copy of RB1, as in this patient's case, remains to be fully elucidated. These results should be interpreted in the clinical context.

PTEN is a tumor suppressor gene, and loss of PTEN results in upregulation of the PI3K/ AKT pathway. Loss of PTEN is most commonly due to promoter hypermethylation, while homozygous deletion and nonsense mutations with loss of heterozygosity (LOH) may also occur. PTEN mutations may occur in multiple exons. Somatic mutations in PTEN have been found in 4--8% of non-small cell carcinomas (NSCLC) including adenocarcinomas and squamous cell carcinomas. This particular variant is likely to be oncogenic. In preclinical studies, PTEN loss is associated with decreased sensitivity of EGFR mutant lung tumors to EGFR TKIs. Clinical trials assessing the efficacy of PI3K inhibitors in PTEN loss are being explored.

Somatic mutations of CDKN2A are present in various tumor types, including, squamous cell carcinoma of the lung, clear cell sarcoma, head and neck cancer, melanoma and esophageal cancer. Majority of the CDKN2A mutations span exon 2 and result in loss or decreased binding to CDK4/6 leading to uncontrolled cell growth through inactivation of Rb and p53 pathways. The D84V mutant is predicted to confer loss of function to the CDKN2A protein as demonstrated by an inability to bind and inhibit the cyclin-dependent kinases CDK4 and CDK6. Multiple preclinical and clinical studies are ongoing for CDKN2A deficient tumors in multiple tumor types.