Gastric Cancer Panel

Gastric cancer is one of the most common cancers worldwide and a leading cause of cancer-related mortality (Sitarz et al. 2018. PubMed ID: 29445300). Similar to other cancers, risk for gastric cancer depends on both genetic and environmental factors (smoking, diet; Sitarz et al. 2018. PubMed ID: 29445300). Identification of pathogenic variants in the germline of gastric cancer patients is important for cancer surveillance (e.g., endoscopy) for the affected individual and family members, since early detection and treatment may decrease morbidity and mortality (Karurah and Huntsman. 2018. PubMed ID: 20301318; NCCN Guidelines Version 2.2022, Gastric Cancer). The vast majority of gastric cancers are considered sporadic; however, approximately 5% to 10% of gastric cancers may be hereditary (Sitarz et al. 2018. PubMed ID: 29445300). Different types of inherited cancer syndromes associated with gastric cancer are described below.

Hereditary Diffuse Gastric Cancer (HDGC): This is a highly penetrant, diffuse-type gastric cancer caused by autosomal dominant germline pathogenic variants in the CDH1 gene and more recently, the CTNNA1 gene (Clark et al. 2020. PubMed ID: 32051609). Patients with HDGC typically present at about 40 years of age and have a cumulative cancer risk of 67% for men and 83% for women by 80 years of age (Pharoah et al. 2001. PubMed ID:11729114).

Familial Adenomatous Polyposis (FAP): FAP is an inherited cancer syndrome characterized clinically by the development of hundreds to thousands of adenomatous polyps in the colon and rectum. If not treated, nearly all FAP patients will develop colorectal cancer (CRC) by age 40 (Fearnhead et al. 2001. PubMed ID: 11257105). Individuals with FAP are also predisposed to desmoid tumors, small bowel cancer, thyroid cancer, hepatoblastoma, and medulloblastoma, as well as upper gastrointestinal tract polyps in the stomach, duodenum, and periampullary regions (Galiatsatos and Foulkes. 2006. PubMed ID: 16454848; Anaya et al. 2008. PubMed ID: 20011437). Upper gastrointestinal tract polyps can lead to gastric cancer (Anaya et al. 2008. PubMed ID: 20011437).

Gastrointestinal stromal tumors (GISTs): GISTs are rare mesenchymal tumors found in the gastrointestinal tract that may be sporadic or familial. Familial GISTs are often distinct from sporadic GISTs in that they are multiple in number, smaller in size, and may present with additional variable features such as interstitial cells of Cajal hyperplasia, dysphagia, hyperpigmentation, urticaria pigmentosa, large hands, lipomas, intestinal neurofibromatosis, and small intestine fibrous tumors (Postow and Robson. 2012. PubMed ID: 23036227).

Hereditary paraganglioma-pheochromocytoma (PGL/PCC) syndrome: PGL/PCC syndrome is a familial cancer syndrome that results in neuroendocrine tumors (Else et al. 2018. PubMed ID: 20301715). Individuals with PGL/PCC syndrome have an increased risk of GIST (Else et al. 2018. PubMed ID: 20301715).

Juvenile Polyposis Syndrome (JPS): JPS is a rare, inherited hamartomatous polyposis syndrome with increased susceptibility to colorectal cancer. Individuals with JPS also have an increased developing gastrointestinal cancer (Howe et al. 1998. PubMed ID: 9869523; Chow and Macrae. 2005. PubMed ID: 16246179).

Li-Fraumeni Syndrome (LFS): LFS is a hereditary cancer syndrome that predisposes individuals to multiple neoplasms at an early age. The most common neoplasms associated with LFS are bone and soft-tissue sarcomas, pre-menopausal breast carcinomas, adrenocortical carcinomas, and brain tumors. Although much less common, melanomas, germ cell tumors, gastric carcinomas, and Wilms tumors have also been described in individuals with LFS (Varley et al. 1997. PubMed ID: 9242456).

Lynch syndrome (LS): Also known as hereditary nonpolyposis colorectal cancer (HNPCC), LS is marked by early onset and a high lifetime risk of cancer, including colorectal, endometrial, gastric, and ovarian cancer (Wagner et al. 2002. PubMed ID: 12203789; Jang and Chung. 2010. PubMed ID: 20559516; Rhees et al. 2014. PubMed ID: 24114314; Mork et al. 2017. PubMed ID: 28004223). Of note, gastric cancer has been reported as the second most common extracolonic cancer in individuals with LS (Win et al. 2012. PubMed ID: 22933731).

Neurofibromatosis type 1 (NF1): NF1 is characterized by cutaneous neurofibromas, café-au-lait spots, iris hamartoma (Lisch nodules), and freckling of axillary and inguinal regions. These features usually become apparent during puberty. Additional features include plexiform neurofibromas, central nervous system gliomas (including optic glioma), macrocephaly, scoliosis, pseudoarthrosis, overgrowth and learning difficulties. A variety of tumors have been observed in individuals with NF1 including gastrointestinal stromal tumors (Friedman. 2019. PubMed ID: 20301288).

Peutz Jeghers Syndrome (PJS): PJS is characterized by hamartomatous polyps in the gastrointestinal tract and melanin pigmentation around the mouth, eyes, nostrils, buccal mucosa, fingers, toes, and other sites. Individuals with PJS also have an increased developing gastrointestinal cancer (Resta et al. 2013. PubMed ID: 23415580; Lindor et al. 2008. PubMed ID: 18559331).

Of note, many of the genes included on this panel are associated with cancer syndromes and significant cancer risk for non-gastric cancers.

The gastric cancer next generation sequencing panel assesses genes that have been shown to be associated with disorders that have gastric cancer as a clinical feature. Genes are organized by inherited cancer syndrome.

Hereditary Diffuse Gastric Cancer (HDGC): Pathogenic variants in CDH1 and CTNNA1 are associated with autosomal dominant HDGC. CTNNA1 encodes alpha-E-catenin, a transmembrane glycoprotein and E-cadherin-partner in the adherens junction complex (Lobo et al. 2021. PubMed ID: 34425242). CDH1 encodes epithelial cadherin (E-cadherin), which is a transmembrane protein that is responsible for cell-to-cell adhesion and cellular invasion suppression. CDH1 also plays important roles in signal transduction, differentiation, gene expression, cell motility, and inflammation (Kaurah and Huntsman. 2018. PubMed ID: 20301318). The activity of E-cadherin in coordination with the actin cytoskeleton through catenins (e.g., α-, β-, and γ-) is responsible for cellular adhesion. Many human cancers show low levels of E-cadherin compared to normal tissue, which causes defects in cellular adhesion and ultimately leads to metastasis. Approximately 10% of gastric cancers show familial clustering, and about 1–3% of cases are known to be hereditary.

Familial Adenomatous Polyposis (FAP): Pathogenic variants in APC are associated with autosomal dominant FAP. APC is a tumor suppressor gene responsible for regulating the Wnt pathway. In FAP tumors, both alleles of APC are inactivated (one inactive allele is inherited and the other occurs somatically [the two hit hypothesis]). The APC protein is responsible for regulation of c-myc, cyclin-D, and cell adhesion and microtubule assembly proteins; absence results in aberrant transcription of these targets (Hegde et al. 2014. PubMed ID: 24310308). More than 1,900 pathogenic variants have been reported in APC (Human Gene Mutation Database), and >90% are nonsense or frameshift mutations that result in a dysfunctional, truncated protein product (Nagase and Nakamura. 1993. PubMed ID: 8111410). Germline pathogenic variants are spread throughout the coding region (Béroud and Soussi. 1996. PubMed ID: 8594558). Several pathogenic variants have also been documented in the promoter, 3’ untranslated region (UTR), and deep within intron 14 (Heinimann et al. 2001. PubMed ID: 11606402).

Gastrointestinal stromal tumors (GISTs): Pathogenic variants in KIT and PDGFRA are associated with autosomal dominant GISTs. While the majority of mutations are found in the KIT gene, several families have been found to have causative mutations in the PDGFRA gene. KIT encodes a tyrosine kinase receptor. The receptor and its ligand, KITLG, function in hematopoiesis, melanogenesis, and gametogenesis (Rothschild et al. 2003. PubMed ID: 12773427). PDGFRA also encodes a tyrosine kinase receptor. Its ligand is platelet-derived growth factor (Maleddu et al. 2011. PubMed ID: 21605429). Ligand binding promotes autophosphorylation of these tyrosine kinase receptors and activation of downstream targets, such as the Ras/MAP kinase, Rac/Rho-JNK, PI3K/AKT, and SFK/STAT signaling networks (Antonescu. 2006. PubMed ID: 17193819; Maleddu et al. 2011. PubMed ID: 2160542). These pathways are involved in cellular differentiation and growth. Deregulation leads to tumorigenesis. The majority of causative germline mutations in the PDGFRA gene are missense variants (Lasota and Miettinen. 2008. PubMed ID: 18312355).

Hereditary paraganglioma-pheochromocytoma (PGL/PCC) syndrome: Pathogenic variants in SDHA, SDHB, SDHC, and SDHD have been associated with autosomal dominant PGL/PCC syndrome. The nuclear genes SDHA, SDHB, SDHC, and SDHD encode the four subunits of the mitochondrial enzyme succinate dehydrogenase (SDH). Pathogenic sequence variants have been reported in SDHA (Else et al. 2018. PubMed ID: 20301715), while pathogenic sequence variants and CNVs have been reported in SDHB, SDHC, and SDHD (Else et al. 2018. PubMed ID: 20301715).

Juvenile Polyposis Syndrome (JPS): Pathogenic variants in BMPR1A and SMAD4 are associated with autosomal dominant JPS. BMPR1A and SMAD4 mediate the biological effects of the transforming growth factor-β (TGF-β) superfamily of cytokines (Miyazono et al. 2010. PubMed ID: 19762341). Pathogenic sequence variants and CNVs have been reported in BMPR1A and SMAD4, with approximately 28% and 27% of JPS cases attributed to variation in each gene, respectively (Haidle and Howe. 2017. PubMed ID: 20301642).

Li-Fraumeni Syndrome (LFS): Pathogenic variants in TP53 are associated with autosomal dominant LFS. TP53 encodes the cellular tumor p53 antigen (Soussi. 2010. PubMed ID: 20930848). p53 is a ubiquitously expressed DNA-binding protein that plays a major role in the regulation of cell division, DNA repair, programmed cell death, and metabolism. More than 500 pathogenic variations have been reported throughout the TP53 gene, and nearly all are detectable by DNA sequencing (Human Gene Mutation Database). Three gross deletions encompassing one or more exons of the TP53 gene have been described but these account for less than 1% of all LFS patients. The risk of developing cancer for carriers of TP53 pathogenic variants has been estimated to be ~73% for men and nearly 100% for women (Chompret et al. 2000. PubMed ID: 10864200).

Lynch syndrome (LS): Pathogenic variants in MLH1, MSH2, MSH6, PMS2, and EPCAM are associated with autosomal dominant LS. MLH1, MSH2, MSH6, and PMS2 are involved in mismatch repair. Pathogenic variants result in defective DNA repair, which leads to cancer (Bujanda and Herreros-Villaneuva. 2017. PubMed ID: 29151953). EPCAM encodes a calcium-independent cell adhesion molecule rather than a mismatch repair protein. Pathogenic variants in MLH1 and MSH2 account for 80-90% of LS and frequently occur in families meeting the stringent Amsterdam I criteria. Pathogenic variants in MSH6 and PMS2 account for most of the remaining LS cases and are often found in families with atypical HPNCC symptoms, such as low rates of MSI or extracolonic carcinomas. Pathogenic variants in EPCAM are typically gross deletions that lead to inactivation of MSH2 via hypermethylation in approximately 1-3% of individuals with LS (Idos and Valle. 2021. PubMed ID: 20301390).

Of note, a germline inversion of exons 1-7 in MSH2 has been reported in fourteen individuals from eleven unrelated families who clinically presented with Lynch syndrome-associated phenotypes including colorectal, endometrial, gastric, and ovarian cancer (Wagner et al. 2002. PubMed ID: 12203789; Rhees et al. 2014. PubMed ID: 24114314; Mork et al. 2017. PubMed ID: 28004223).

Neurofibromatosis type 1 (NF1): Pathogenic variants in NF1 are associated with autosomal dominant neurofibromatosis type 1. De novo pathogenic variants are frequent. NF1 encodes the neurofibromin protein, a negative regulator of the RAS/MAPK pathway. Over 2,000 NF1 germline variants have been reported and include all types. Large deletions account for ~5% of patients with NF1 and are usually associated with a severe phenotype (Friedman. 2019. PubMed ID: 20301288). Gross insertions and complex rearrangements are rare.

Peutz Jeghers Syndrome (PJS): Pathogenic variants in STK11 are associated with autosomal dominant PJS. STK11, also called LKB1, encodes a serine/threonine kinase that inhibits cellular proliferation by promoting cell-cycle arrest (Tiainen et al. 1999. PubMed ID: 10430928). Most pathogenic variants (80%) are truncating pathogenic variants (frameshift, nonsense, splice-site, or exonic deletions) that result in early protein termination (Hearle. 2006. PubMed ID: 16707622). The remaining pathogenic variants are mostly missense or in-frame deletions. Large genomic deletions in STK11 have been described.

See the individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

Clinical sensitivity of tested genes is given based on each disorder.

Hereditary Diffuse Gastric Cancer (HDGC): The clinical sensitivity of CDH1 germline pathogenic variants is 30% for HDGC families (Carneiro et al. 2007. PubMed ID: 17513507). Large deletions have been detected in the CDH1 gene in up to 4% of patients (Kaurah and Huntsman. 2014. PubMed ID: 20301318). The clinical sensitivity of CTNNA1 is presently unknown (Clark et al. 2020. PubMed ID: 32051609; Lobo et al. 2021. PubMed ID: 34425242).

Familial Adenomatous Polyposis (FAP): This test is predicted to detect >90% of causative APC pathogenic variants (Laken et al. 1999. PubMed ID: 10051640). Gross deletions/duplications have been reported in up to 12% of APC patient samples (Jasperson et al. 2017. PubMed ID: 20301519).

Gastrointestinal stromal tumors (GISTs): Approximately 90% of individuals with familial GISTs will have a mutation in the KIT and PDGFRA genes. PDGFRA causative mutations are found in approximately a third of patients who test negative for KIT mutations (Antonescu. 2006. PubMed ID: 17193819).

Hereditary paraganglioma-pheochromocytoma (PGL/PCC) syndrome: Although the majority of PGL/PCC syndrome tumors are sporadic, approximately 13% are associated with germline pathogenic variants in known PGL/PCC syndrome genes (Welander et al. 2011. PubMed ID: 22041710).

Juvenile Polyposis Syndrome (JPS): This test is predicted to identify a BMPR1A pathogenic variant in 11-22% and a SMAD4 pathogenic variant in 20-26% of patients diagnosed with JPS. CNV analysis is predicted to identify a BMPR1A pathogenic variant in 1-2% and a SMAD4 pathogenic variant in 2-9% of patients diagnosed with JPS (Larsen Haidle and Howe. 2017. PubMed ID: 20301642).

Li-Fraumeni Syndrome (LFS): Sequencing the TP53 gene yields positive results for approximately 95% of patients with LFS. Deletions in the TP53 gene have been detected in 1% of LFS cases (Schneider et al. 2019. PubMed ID: 20301488).

Lynch Syndrome (LS): The clinical sensitivity of EPCAM deletions is 1-3% of individuals with LS (Idos and Valle. 2021. PubMed ID: 20301390). LS is also attributed to deletions in the MLH1, MSH2, MSH6, and PMS2 genes in approximately 5%, 20%, 7%, and 20% of cases, respectively (Idos and Valle. 2021. PubMed ID: 20301390).

Neurofibromatosis type 1 (NF1): This test will detect pathogenic variants in NF1 in 80-93% of patients that meet the NIH clinical diagnostic criteria for neurofibromatosis type 1 (Maruoka et al. 2014. PubMed ID: 25325900; van Minkelen et al. 2014. PubMed ID: 23656349; Pasmant et al. 2015. PubMed ID: 25074460; Zhang et al. 2015. PubMed ID: 26056819; Calì et al. 2017. PubMed ID: 27838393). Deletions and duplications of NF1 represent ~5% of cases (Friedman. 2019. PubMed ID: 20301288).

Peutz-Jeghers Syndrome (PJS): Approximately 55% of patients with a positive family history and 70% of patients with no family history of PJS will receive positive results through STK11 sequencing. Approximately 45% of patients with a positive family history or 21% of patients with no family history of PJS will have a pathogenic variant in STK11 by deletion analysis (McGarrity et al. 2016. PubMed ID: 20301443).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.97% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. 

Deletion and duplication detection for NF1, STK11 and PMS2 is performed using NGS, but CNVs detected in these genes are confirmed via multiplex ligation-dependent probe amplification (MLPA).

DNA analysis of the PMS2 gene is complicated due to the presence of several pseudogenes. One particular pseudogene, PMS2CL, has high sequence similarity to PMS2 exons 11 to 15 (Blount et al. 2018. PubMed ID: 29286535). Next-generation sequencing (NGS) based copy number variant (CNV) analysis can detect deletions and duplications involving exons 1 to 10 of PMS2 but has less sensitivity for exons 11 through 15. Multiplex ligation-dependent probe amplification (MLPA) can detect deletions and duplications involving PMS2 exons 1 to 15. Of note, PMS2 MLPA is not typically included in this test but can be ordered separately using test code 6062, if desired. 

This test also includes analysis of the inversion of exons 1-7 in MSH2.

Of note, Next Generation Sequencing analysis of the SDHA gene is technically challenging due to the presence of segmental duplications and paralogy. Therefore, analysis of CNVs in this region is not included in this test.