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.

Germline APC mutations are characteristically associated with Familial Adenomatous Polyposis (FAP) that predisposes to carcinomas of the colo-rectum, stomach, duodenum, and thyroid. Recently somatic mutations in exon 15 of APC gene have been described in certain sporadic papillary thyroid carcinomas. The prognostic impact of these mutations remains unknown in such settings.

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 rightly considered to be a tumour suppressor, ATM signalling can also be advantageous to cancer cells, particularly in resistance to radio- and chemotherapeutic treatment. For this reason, ATM inhibitors have been developed for use in cancer therapy.

Eighty percent of all thyroid cancers are papillary thyroid carcinomas (PTCs). BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and V600E is an activating mutation of BRAF. The BRAF V600E mutation has been reported in 45% of patients with papillary thyroid carcinoma. The BRAF V600E-like PTC's (BVL) and the RAS-like PTC (RL-PTC) are fundamentally different in their genomic, epigenomic, and proteomic profiles. Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC , other well-differentiated thyroid neoplasms or nodular goiters. The possible prognostic impact of BRAF V600E mutations in papillary carcinoma of the thyroid continues to be studied. FDA approved dabrafenib and trametinib administered together for the treatment of BRAF V600E mutation-positive anaplastic thyroid cancer.

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. In thyroid, RAS (HRAS, NRAS and KRAS) mutations are identified in 10--20% of papillary carcinomas, 40--50% of follicular carcinomas, 10% of medullary carcinomas, and 20--40% of poorly differentiated and anaplastic carcinomas. The frequency of HRAS mutations in thyroid carcinomas is approximately 4%. HRAS mutations at codon 61 have been reported in a variety of thyroid lesions and are especially prevalent in the follicular variant of papillary thyroid carcinoma. However, the predictive or prognostic significance of HRAS mutation in thyroid carcinoma is not clear and correlation with other clinical and laboratory findings is necessary.

RAS mutations (HRAS, NRAS and KRAS) are found in all epithelial thyroid malignancies. The frequency of HRAS mutations in thyroid carcinomas is 4%. RAS mutations are identified in 10-20% of papillary carcinomas, 40-50% of follicular carcinomas and 20-40% of poorly differentiated and anaplastic carcinomas .

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 the most common type of RAS mutations in thyroid nodules. Activating point mutations in NRAS gene have been associated with follicular-patterned neoplasms including follicular adenoma, follicular carcinoma and follicular variant papillary thyroid carcinoma cases. NRAS mutations have been also detected in a subset of poorly differentiated carcinoma and anaplastic carcinoma. NRAS mutations concentrate in codon 61, while those in codons 12 or 13 are rare. According to some studies, there is a significant correlation between RAS mutations and distant bone metastases among follicular and papillary carcinomas. However, RAS mutations are also frequently found in encapsulated follicular variant of papillary carcinoma, a tumor with an indolent behavior. Clinical correlation is recommended.

RAS mutations have also been identified in benign Follicular Adenomas(FA); however, it is unclear whether RAS positive FA have a higher chance of progression to cancer. The prevalence of this mutation in benign thyroid nodules is between 20 and 40%. The low overall prevalence of RAS mutations in thyroid cancers and the relatively high mutation rate in benign nodules makes ras mutation analysis unsuitable as a standalone test to predict malignancy in indeterminate thyroid nodules.

Somatic mutations in PIK3CA are seen in approximately 2% of papillary thyroid carcinoma, poorly differentiated carcinoma, anaplastic carcinoma. Somatic mutations of PIK3CA have been described particularly in advanced and dedifferentiating thyroid tumors. Their prevalence varies from 16 to 23% in anaplastic thyroid carcinomas. They are less frequent in papillary and follicular thyroid carcinomas and the prevalence in medullary thyroid carcinomas remains unknown. Although inhibitors of the PI3K/AKT/mTOR pathway have shown efficacy against thyroid cancer in pre-clinical models, their success in clinical trials remains to be determined.

MET is a member of the receptor tyrosine kinase and proto-oncogene playing a major role in tumor development and metastasis. MET E168D has been previously reported in papillary thyroid carcinoma. This mutation is located in the SEMA domain containing the ligand binding site. In vitro study has shown that E168D alters MET functionality in lung cancer. The prognostic and predictive significance of MET mutations in thyroid cancer is not clear and correlation with other clinical and laboratory findings is necessary. Of note, this variant is reported as a likely benign germline variant in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/41627/).

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. 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 15% of anaplastic thyroid cancer. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome. Patients with Cowden syndrome have an increased risk of developing epithelial thyroid cancer, follicular carcinoma being the most common, of up to 10% compared to <1% in the general population. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.

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. This mutation has seen more frequently in thyroid carcinomas than in the goiter controls. But its significance has been challenged by other studies which report a low incidence of T1010I mutation in both tumors and controls and not resulting in an enhanced c-MET phosphorylation. The utility of MET pathway inhibitors also continues to be explored. 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/).

This mutation, namely a 1795GTT insertion, results in BRAF V599Ins. Kinase assays on BRAF V599Ins and BRAF V600E show increased enzymatic activity, increased phosphorylation of MEK, MAPK and RSK and a high transformation rate in the cells compared to wild type BRAF. Thus, BRAF V599Ins, similar to BRAF V600E, is a 'gain of function' mutation, with constitutive activation, which accounts for its role in papillary cancer of the thyroid.

RAS mutations (HRAS, NRAS and KRAS) are found in all epithelial thyroid malignancies. The frequency of KRAS mutations in thyroid carcinomas is 2-3%. Overall, RAS mutations are identified in 10--20% of papillary carcinomas (follicular variant), 40--50% of follicular carcinomas and 20--40% of poorly differentiated and anaplastic carcinomas. Of note, RAS point mutations are mutually exclusive with other thyroid mutations such as BRAF, RET/PTC, or TRK rearrangements in papillary thyroid cancers. In follicular carcinomas, RAS mutations are mutually exclusive with PAX8-PPARG rearrangements. RAS mutations have also been associated with more aggressive disease and distant metastasis. The therapeutic implications of RAS mutations in thyroid cancer are unknown at this time.

Smad4 is tumor suppressor gene and is crucial for thyroid development and function. It is key component of the transforming growth factor beta (TGFB) pathway which regulates the expression of thyroid-specific genes. The role of SMAD4 in thyroid tumorigenesis remains unclear. However, mutations affecting the coding region of the SMAD4 gene have been detected in some sporadic thyroid neoplasms. Studies that analyzed expression of SMAD4 in thyroid tumors gave contradictory results. Some studies showed that the expression of SMAD4 was reduced in thyroid cancer cells. Other studies indicated that it was expressed and present in the nucleus in all thyroid cell lines and controls analyzed, indicating propagation of TGFB signaling in thyroid tumors. Of note, a SMAD4 mutation C324Y, recently isolated from nodal metastases of papillary thyroid carcinoma (PTC), was confirmed to cause an increase in TGFB signaling and lead to the acquisition of transformed phenotype and invasive behavior in thyroid cells, enabling them to proliferate independently from thyroid-stimulating hormone.

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. Eighty percent of all thyroid cancers are papillary thyroid carcinomas (PTCs). Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC and other well-differentiated thyroid neoplasms or nodular goiters. The K601E mutation results in an amino acid substitution at position 601 in BRAF, occurring within the highly conserved motif of the kinase domain. This is the second most common BRAF mutation found in thyroid nodules after V600E. Unlike BRAF V600E, K601E is strongly associated with follicular-patterned cancer, particularly with the encapsulated follicular variant of PTC, and may also be found in follicular thyroid carcinomas. Overall, BRAF K601E mutant tumors may show better clinical outcomes than BRAF V600E positive tumors.

MLH1 is a component of the cellular DNA mismatch repair (MMR) machinery causing hereditary nonpolyposis colorectal cancer (HNPCC), and is associated with specific somatic alterations in the tumor, characterized by high microsatellite instability (MSI-H). 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 in thyroid tumors. However, some other MLH1 variants have been described in some thyroid tumors, but their clinical significance is yet to be determined. Of note, according to one report, MLH1 V384D variant has been reported to be associated with primary resistance to EGFR-TKIs in patients with EGFR L858R-positive lung adenocarcinoma. Clinical correlation is recommended.

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. 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 (deletion, mutation, and methylation) in p16 associated with loss of function have been reported in cell lines and primary thyroid tumors. However, predictive or prognostic significance of p16 in thyroid cancer is not clear and correlation with other clinical and lab findings is necessary. Multiple clinical trials are available for patients with CDKN2A deficient tumors.

EGFR mutations have been reported in 1-3% of thyroid cancers. The prognostic and predictive significance of EGFR mutations in thyroid cancer is not clear and correlation with other clinical and laboratory findings is necessary. Clinical trials involving protein kinase inhibitor are available for patients with tumors harboring EGFR mutations.

Although CEBPA mutations have been described in AML, the significance of this mutation in this tumor is unclear.

Although CEBPA mutations have been described in AML, the significance of this mutation in this tumor is unclear.

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.

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. Codon I1307 lies within a regulatory region of the APC protein mediated by ubiquitination. Germline 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. APC somatic mutations are found in less than 1% of thyroid carcinomas. The I1307K has not been reported as a somatic mutation in thyroid carcinoma to date. The prognostic and therapeutic implications of somatic APC mutations in thyroid carcinoma remain to be fully elucidated. Correlation with other clinical and lab findings is recommended.

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.

Proto-oncogene tyrosine-protein kinase receptor RET, activates the MAPK pathway for cell proliferation and the PI3K/AKT pathway for cell survival. RET activating mutations and rearrangements are common in medullary thyroid carcinomas. 25-30% of medullary thyroid carcinomas are associated with germline RET mutations. In these germline mutations, the most commonly affected codons are 609, 611, 618, 620 (exon 10) and 634 (exon 11), encoding for the extracellular cysteine-rich domain, and codons 768 (exon 13) and 804 (exon 14) of the intracellular tyrosine kinase domain. Sporadic RET mutations have been reported in 61.5% of medullary thyroid carcinomas. In sporadic cases, the M918T mutation is most commonly reported and may indicate a poor prognosis. Given these identified molecular alterations, therapies targeting the RET signaling pathway have been used and shown to provide advantages over traditional cytotoxic therapy with regard to disease response. There are multiple ongoing clinical trials on cabozantinib (tyrosine kinase inhibitor), sorafenib (multikinase inhibitor), and everolimus (mTOR inhibitor).

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.

BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and is frequently mutated in papillary thyroid carcinoma (PTC). The BRAF V600E-like PTC's (BVL) and the RAS-like PTC (RL-PTC) are fundamentally different in their genomic, epigenomic, and proteomic profiles. The BRAF V600E mutation in Exon 15 is the most common BRAF mutation has been reported in 45% of patients with PTC. BRAF F468S is a rare somatic variant in Exon 11 and is located in the tyrosine kinase domain of the BRAF protein. The clinicopathologic effects of this variant as a somatic mutation in cancer has not been established in the literature. However, a mutation at the same location, F468C, has been shown to be a gain of function mutation. This variant has also been previously reported as a pathogenic germline variant in ClinVar associated with Cardio-facio-cutaneous syndrome. These results should be interpreted in the clinical 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. 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 15% of anaplastic thyroid cancer. Germline mutations of PTEN lead to inherited hamartoma and Cowden syndrome. Patients with Cowden syndrome have an increased risk of developing epithelial thyroid cancer, follicular carcinoma being the most common, of up to 10% compared to <1% in the general population. The PTEN I101T has been observed in a variety of cancer types. One study identified the PTEN I101T variant in 1 out of 172 patients with germ line PTEN mutations. Of note, an in vitro studied observed that the PTEN I101T variant reduced the half-life of PTEN as well as significantly reduced its activity. Clinical trials using PI3K-beta inhibitor are available for patients with PTEN-deficient tumors.

The Mesenchymal Epithelial Transition (MET) proto-oncogene encodes the MET receptor tyrosine kinase, also called c-MET or hepatocyte growth factor (HGF) receptor. MET is a ubiquitously expressed cell surface receptor that leads to the activation of several downstream intracellular pathways which promote cellular growth and proliferation, motility, migration and angiogenesis. Dysregulation of MET via gene amplification, germline or somatic mutations or receptor overexpression has been observed in a variety of epithelial cancers, including breast prostate cancer, non-small cell lung cancer, renal papillary carcinoma, hepatocellular and gastric carcinomas. Genetic alterations in MET have been identified in 0.4% of thyroid carcinomas. The prognostic and predictive significance of MET mutations in thyroid cancer is not clear and correlation with other clinical and laboratory findings is necessary. M362T has been identified in the scientific literature, but has not been biochemically characterized and therefore, its effect on protein function is unknown. This variant is reported as a benign/likely benign germline variant in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/93565).

BRAF is part of the mitogen-activated protein kinase (MAPK) signaling pathway and V600E is an activating mutation of BRAF. The BRAF V600E mutation has been reported in 45% of patients with papillary thyroid carcinoma, which comprise 80 % of all thyroid cancers. Presence of a BRAF p.Val600Glu (V600E) mutation is highly specific for papillary thyroid carcinoma and is only rarely associated with the follicular variant PTC, other thyroid neoplasms, or nodular goiters. Anaplastic thyroid carcinomas are rare, highly aggressive, undifferentiated tumors that comprise 1% to 2% of all thyroid cancers in the United States. Well-differentiated papillary thyroid cancer, in which BRAF V600 mutations are an early and common driver mutation, precedes or coexists with approximately 50% of anaplastic thyroid carcinomas. Between 20% and 50% of anaplastic thyroid carcinomas harbor activating BRAF V600 mutations, with unknown prognostic significance. The possible prognostic impact of BRAF V600E mutations in carcinoma of the thyroid continues to be studied.

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/).

JAK2 is a non-receptor tyrosine kinase that mediates signaling via the JAK-STAT pathway and the somatic, activating mutation V617F in the pseudokinase domain of JAK2 has been reported in over 90% of patients with polycythemia vera, 40-70% of essential thrombocytemia and 40-60% of primary myelofibrosis. JAK2 mutations have not been described in papillary thyroid carcinomas. Moreover, this variant has high prevalence in the East Asian population, and thus is predicted be a germline variant. Clinical correlation with other laboratory findings is recommended.

NOTCH1 is a transmembrane receptor, which plays a role in cell fate determination, growth, and survival. Somatic alterations in NOTCH1 are very rare in thyroid carcinomas 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.

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 are seen in approximately 2% of papillary thyroid carcinoma, poorly differentiated carcinoma, anaplastic carcinoma. Somatic mutations of PIK3CA have been described particularly in advanced and dedifferentiating thyroid tumors. Their prevalence varies from 16 to 23% in anaplastic thyroid carcinomas. They are less frequent in papillary and follicular thyroid carcinomas and the prevalence in medullary thyroid carcinomas remains unknown. Although inhibitors of the PI3K/AKT/mTOR pathway have shown efficacy against thyroid cancer in pre-clinical models, their success in clinical trials remains to be determined.