EGFR mutations in GBM cluster in the extracellular (EC) domain and include in-frame deletions (such as the common “variant III” del 6-273) and missense mutations (A289V, A289D, T263P, G598V). In vitro and in vivo studies reveal anchorage-independent growth and tumorigenic potential when the A289 and G598 variants are stably expressed in NIH-3T3 cells. The A289 and G598 mutations sensitize Ba/F3 cells to erlotinib in vitro according to some reports, although other reports state glioma-specific EGFR EC mutants are poorly inhibited by EGFR inhibitors that target the active kinase conformation (e.g., erlotinib). The A289 variant has been reported to show sensitivity towards BAY846, a tyrosine kinase inhibitor in brain tumors. In addition, according to some reports, inhibitors which bind to the inactive EGFR conformation potently inhibit EGFR EC mutants and induce cell death in EGFR mutant GBM cells.

In GBM, EGFR mutations typically cluster in the extracellular domain and include in-frame deletions (such as the common “variant III” del 6-273) and missense mutations (A289V, A289D, T263P, G598V). EGFR exon 20 insertions have not been previously reported in GBM. The clinical significance of this mutation with regards to response to anti-EGFR therapy in GBM is unknown. In general, EGFR exon 20 mutations have been reported in approximately 9% of all EGFR-mutated cases of lung cancer and studies show that in contrast to the more classic activating EGFR mutations, these insertions have been associated with de novo resistance or only partial response to approved EGFR-TKIs (erlotinib and gefitinib) in lung cancer.

In GBM, EGFR mutations typically cluster in the extracellular domain and include in-frame deletions (such as the common “variant III” del 6-273) and missense mutations (A289V, A289D, T263P, G598V). However, the p.E709K mutation in the tyrosine kinase domain of EGFR has not been previously reported in GBM. In vitro functional characterization of mutations at E709 have been reported to be activivating mutations that are associated with sensitivity to EGFR inhibitors in vitro in some cell systems. The clinical significance of this mutation with regards to response to anti-EGFR therapy in GBM is unknown.

Greater than 40% of glioblastomas (GBM) harbor focal amplification of the EGFR locus and there is evidence to suggest that these are driver alterations in these patients, making the EGFR pathway a potential therapeutic target in some clinical settings. Moreover, this alteration is relatively specific for GBM with very few other diffusely infiltrative gliomas having been shown to carry focal amplification of this locus (<3%). In GBM, this alteration frequently occurs in combination with other alterations of EGFR including polysomy 7, intragenic inframe deletions (e.g. EGFRvIII), and/or somatic point mutations. Based on current evidence, the independent predictive value of EGFR amplification in GBM is unclear. The relationship between individual and concurrent EGFR alterations and clinical response to small molecular inhibitors targeting EGFR is currently under investigation in clinical trials.

IDH1 or IDH2 mutations are found in >70% of lower grade diffusely infiltrative gliomas and in >90% of secondary glioblastoma. IDH mutational status has been reported to be a favorable prognostic indicator relative to wild-type gliomas of similar histology, regardless of grade. Therapeutic strategies exploiting mutated IDH protein, including through direct inhibition and vaccine-based approaches, are currently the subject of preclinical research and clinical trials.

IDH1 or IDH2 mutations are found in >70% of lower grade diffusely infiltrative gliomas and in >90% of secondary glioblastoma. IDH mutational status has been reported to be a favorable prognostic indicator relative to wild-type gliomas of similar histology, regardless of grade. Therapeutic strategies exploiting mutated IDH protein, including through direct inhibition and vaccine-based approaches, are currently the subject of preclinical research and clinical trials.

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.

PTEN is an obligate haplo-insufficient tumor suppressor gene and is mutated in a large number of cancers. It encodes a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Most PTEN mutations are loss-of-function mutations. Mono-allelic or bi-allelic loss of PTEN is found in a considerable fraction of tumors, including gliomas (75%). In glioblastoma, PTEN loss/deletion is associated with poor patient prognosis, and/or shorter disease-free survival. There are ongoing clinical trials investigating anti-tumor activity of agents in recurrent glioblastoma with this mutation.

MET is frequently overexpressed in glioblastomas (GBM), and some gliomas show hepatocyte growth factor (HGF) autocrine activation of the MET signaling pathway. Several studies have found that HGF and MET are expressed at higher levels in human gliomas than in control brain tissue, and that expression levels correlate with tumor grade. Some studies have shown that the HGF expression in high-grade (WHO Grade III-IV) tumors was significantly higher than in low-grade (WHO I-II) tumors. Similarly, coexpression of HGF and MET is observed more frequently in Grade IV GBM than in low-grade glioma, consistent with the contribution of an HGF/MET autocrine loop to malignant progression in these tumors. However, MET sequence alterations have been rare. The p.T1010I mutation, in the cytoplasmic juxtamembrane domain of MET has been reported in some tumor types and also has been reported as a germline variant present in less than 1% of the general population. Its role in tumor development and progression continues to be studied. The utility of MET pathway inhibitors also continues to be explored.

The APC gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. APC promotes rapid degradation of beta-catenin and participates in Wnt signaling as a negative regulator. APC is also involved in other processes including cell migration, cell adhesion, transcriptional activation and apoptosis. Germline defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. Somatic mutations in this gene may be observed in colorectal cancer (CRC), stomach cancer and desmoid tumors. Although APC mutations have been reported in up to 5% of low grade gliomas and up to 13% primary glioblastomas (GBM), evidence regarding their involvement in CNS tumors is still limited. Further studies are needed to explore the clinical value of these mutations in CNS tumors.

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).

The SEPT14 gene has been described as a fusion partner with EGFR in up to 4% of glioblastomas. In that context, glioma cell lines harboring this gene fusion were found to be susceptible to EGFR inhibitors in vitro. The functional significance of an isolated partial amplification of this gene would be of uncertain significance. Detection of rearrangement of this locus with a fusion partner such as EGFR would require an alternative methodology such as RNAseq or FISH analysis.

The CDKN2A gene locus is altered in up to approximately 57% of glioblastoma, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2B locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials.

The CDKN2B gene locus is altered in up to approximately 55% of glioblastoma, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2A locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials.

The PTPN11gene encodes SHP-2, a widely expressed cytoplasmic protein tyrosine phosphatase. SHP-2 is essential for activation of the RAS/MAPK signaling cascade. Most mutations are gain-of-function and result in prolonged ligand-dependent activation of the RAS/MAPK cascade. Germ-line PTPN11 mutations cause Noonan syndrome, a developmental disorder characterized by an increased risk of malignancies. Activating somatic mutations in PTPN11 have been documented in certain hematologic malignancies but they are infrequent in solid tumors. According to TCGA data base, about 2% of all the glial tumors harbor somatic mutations in PTPN11 gene but their prognostic and therapeutic significance remains to be fully elucidated. The utility of SHP2 inhibitors continues to be explored in some preclinical studies.

The protein encoded by the RB1 gene is a negative regulator of the cell cycle and was the first tumor suppressor gene identified. The active, hypophosphorylated form of the protein binds transcription factor E2F1. RB1 alterations including mutations and deletions are seen in up to 11% of glioblastomas. It has been suggested that patients with RB1-deficient tumors do not respond to cyclin-dependent kinase (CDK) inhibitors. The predictive and prognostic significance of RB1 mutations in glioblastoma needs to be further studied.

In AML, presence of exon 17 mutations in KIT may confer an adverse prognosis or increased relapse rate. However, its significance in brain tumors is yet to be determined.

FGFR2 mutation in a patient with oral squamous cell carcinoma was associated with response to the multitargeted tyrosine kinase inhibitor pazopanib. The clinical significance of this finding in this tumor type is unknown.

EGFR mutations have been reported in up to 21% of glioblastoma tumors (GBM). In GBM, EGFR mutations typically cluster in the extracellular domain and include in-frame deletions and missense mutations. However, mutations (such as V774M) in the tyrosine kinase domain of EGFR have been previously reported in GBM. The clinical significance of this mutation with regards to response to TKI therapy in GBM needs further elucidation. Results should be interpreted in conjunction with other laboratory and clinical findings.

MET is a member of the receptor tyrosine kinase and proto-oncogene playing a major role in tumor development and metastasis. MET mutations have been reported in up to 3.3% of low-grade gliomas and 2.2% of glioblastomas. MET E168D mutation is located in a conserved domain containing the ligand binding site. In vitro studies have shown that E168D may be associated with higher ligand affinity and higher susceptibility to c-Met inhibitors in lung cancer. The predictive and prognostic significance of MET mutations in brain tumors is unclear and needs to be further studied. Correlation with other clinical and laboratory findings is recommended.

EGFR mutations in GBM cluster in the extracellular (EC) domain and include in-frame deletions (such as the common “variant III” del 6-273) and missense mutations (A289V, A289D, T263P, G598V). Mutations involving residue R108 have been reported in GBM, frequently occurring with other EGFR mutations at amino acids A289, P596, and G598. In vitro studies have shown that R108K mutation leads to increased ligand-binding affinity and shows anchorage-independent growth and tumorigenic potential when stably expressed in NIH-3T3 cells. The predictive and prognostic significance of this mutation at R108 needs further elucidation. Correlation with other clinical and laboratory findings is recommended.

PDGFRA amplification is reportedly present in up to 29% of pediatric and 21% of adult high-grade astrocytomas when assessed by fluorescent in situ hydridization. Copy number alterations of this gene have been reported in approximately 11% of adult glioblastoma making it the second most commonly altered receptor tyrosine kinase after EGFR. In those adult glioblastomas that are IDH-mutant, there is evidence to suggest that amplification of PDGFRA is associated with worse overall survival.

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 H83Y lies within the ANK3 domain of the CDKN2A protein. H83Y confers a loss of function to the CDKN2A protein as demonstrated by loss of cell cycle control. The CDKN2A gene locus is altered in up to approximately 57% of glioblastoma, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2B locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials. CDKN2A mutations account for only 1-3% of glioblastomas and the clinical significance remains to be elucidated.

SMAD4 is tumor suppressor gene and it encodes an intracellular mediator in the transforming growth factor b (TGF b) signal transduction pathway. Somatic mutations in SMAD4 are exceedingly rare in glial neoplasms. SMAD4 I525V has been reported as a likely benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/41788/). These results should be interpreted in the clinical context.

NRAS gene belongs to the family of RAS genes. It encodes a G protein that is important in the transmission of growth-promoting signals from the cell surface receptors to the nucleus through RAS-RAF-mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)-AKT cell signaling pathways. NRAS mutations are rare in glial neoplasms and are found in about 1% of cases. The clinicopathologic significance of NRAS mutations in glial neoplasms remains to be further elucidated.

The CDKN2A gene locus is altered in up to approximately 57% of glioblastoma, most commonly as a homozygous deletion, and frequently with concurrent deletion of the CDKN2B locus. CDKN2A/CDKN2B loss may be associated with increased sensitivity to CDK4/6 inhibitors. W110* results in early truncation and confers a loss of function as demonstrated by loss of CDK binding and cell cycle control in culture. The clinicopathologic effects of the heterozygous rather than homozygous loss of CDKN2A in glial neoplasms remains to be further elucidated. The efficacy and toxicity profiles of these inhibitors in the context of a variety of cancer types are currently under evaluation in clinical trials.

MLH1 is a component of the cellular DNA mismatch repair (MMR) machinery. The MLH1 V384D mutation has been associated with cancer risk in some tumor types. This variant encodes in a partially impaired protein with diminished interaction with PMS2 protein and reduced MMR activity in vitro. The MLH1 V384D variant has not been reported as a somatic mutation in glial brain tumors. This variant has an allele frequency of 4% in the East Asian population. Some studies have shown that patients carrying the MLH V384D variant have an increased risk of the development of microsatellite-instable as well as -stable colorectal cancer. MLH1 V384D variant has also been reported to be associated with primary resistance to EGFR-TKIs in patients with EGFR L858R-positive lung adenocarcinoma. Of note, this variant is reported as a benign germline variant in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/41632/). Clinical correlation is recommended.

PDGFRA amplification is reportedly present in up to 29% of pediatric and 21% of adult high-grade astrocytomas when assessed by flourescent in situ hydridization. Copy number alterations of this gene have been reported in approximately 11% of adult glioblastoma making it the second most commonly altered receptor tyrosine kinase after EGFR. In those adult glioblastomas that are IDH-mutant, there is evidence to suggest that amplification of PDGFRA is associated with worse overall survival. Somatic mutations within the PDGFRA gene are less frequent than amplifications. PGDFRA N659K is within the tyrosine kinase domain and confers a gain of function. Preclinical trials in N659K mutant cell lines have shown sensitivity to multi-targeted tyrosine kinase inhibitors including imatinib and crenolanib.

SMAD4 is a tumor suppressor gene and it encodes an intracellular mediator in the transforming growth factor b (TGF b) signal transduction pathway. SMAD4 mutations are very rare in glioblastoma and are present in less than 1% of cases and the significance of these mutations are unclear in this tumor type. The effect on protein function of SMAD4 P472T remains to be further elucidated. These results should be interpreted in the clinicopathologic context.

PTEN is an obligate haplo-insufficient tumor suppressor gene and is mutated in a large number of cancers. It encodes a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/mTOR signaling pathway. Most PTEN mutations are loss-of-function mutations. Mono-allelic or bi-allelic loss of PTEN is found in a considerable fraction of tumors, including gliomas (75%). In glioblastoma, PTEN loss/deletion is associated with poor patient prognosis, and/or shorter disease-free survival. The PTEN P169H mutation, however, is not definitively known to cause a loss-of-function change in the PTEN protein and has been shown to confer a phosphatase activity similar to wild-type PTEN in yeast. This variant has been identified in one case of glioblastoma according to the literature. This result should be interpreted in the clinicopathologic context.

KIT, also known as proto-oncogene c-Kit or tyrosine-protein kinase Kit or CD117, is a growth factor receptor of the tyrosine kinase subclass III family, normally expressed in a variety of tissue types. Signaling through CD117 plays a role in cell survival, proliferation, and differentiation. KIT is found in approximately 1% of glioblastomas. The KIT D45N variant is in the extracellular domain, however, its effect on protein function is unknown. The clinical significance of KIT in glioblastoma and the clinicopathologic effect of this variant remains to be further elucidated.

CDH1 on 16q22.1 encodes E-cadherin which functions in intercellular adhesion. E-cadherin is involved in transmitting chemical signals and controlling cell maturation and movement, and acts as a tumor suppressor. CDH1 is rare in this tumor type and is found in approximately 1% of glioblastomas. The CDH1 A403T variant has not been characterized in the literature and therefore has an unknown effect on protein function and is best classified as a variant of uncertain significance (VUS). The clinical significance of CDH1 in glioblastoma is unknown and its clinicopathologic effect remains to be further elucidated.

BRAF alterations have been described in a wide spectrum of brain tumors, including in gliomas and glioneuronal tumors. BRAFV600E mutations have been found in approximately 10--15% of pilocytic astrocytoma and in approximately 5--10% of pediatric diffusely infiltrating gliomas, including diffuse astrocytomas (WHO grade II), anaplastic astrocytomas (WHO grade III) and glioblastomas (WHO grade IV), but in less than 2% of comparable adult gliomas. This mutation is potentially targetable.

H3F3A K28M mutation (more commonly referred to as K27M) is a diagnostic parameter for the 2016 WHO-recognized entity, "Diffuse Midline Glioma H3 K27M-mutant", an astrocytic diffusely infiltrating tumor arising in the midline, typically within the brainstem, but also sometimes arising in the diencephalon or spinal cord. These tumors have a poor prognosis. The H3K27M alteration, which is characteristically heterozygous, leads to a decrease in overall H3K27me3 levels through dysregulation of the polycomb repressive complex 2 (PRC2), and a concurrent increase in H3K27 acetylation levels. Research is ongoing in an effort to develop ways to exploit this characteristic molecular alteration through targeted strategies.