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CLINICAL CAPABILITIES // Genetic testing

Gastric

Identify genetic risk factors and causes of gastric cancer.

Clinical at Psomagen

Who Would Benefit from Gastric Cancer Genetic Testing?

1

A person with a strong family history of certain types of cancer

Determine if they carry a gene mutation that increases their risk. If they do have an inherited mutation, they might want to have screening tests to look for cancer early, or even take steps to try to lower their risk.

2

A person already diagnosed with cancer

This is especially true if there are other factors to suggest the cancer might have been caused by an inherited mutation (such as a strong family history or if the cancer was diagnosed at a young age). Genetic testing might show if the person has a higher risk of developing cancer. It can also help other family members decide if they want to be tested for the mutation.  

3

Family members of a person known to have an inherited gene mutation that increases their risk of cancer

Testing can help them know if they need screening tests to look for cancer early, or if they should take steps to try to lower their risk.

How Do I Order a Test?

A printed copy of the requisition form must be submitted with the specimen if you are not placing your order through the online portal. You can find and print a copy of the requisition form here. If you need to modify your order, please contact client services.

Gastric Panel Best Practices

Preferred Specimen

2mL whole blood in a purple-top EDTA tube (K2EDTA or K3EDTA)

Alternate Specimens

  • Saliva
  • Buccal swab
  • gDNA
Let's get started!

How to Ship Your Samples

Follow IATA Regulations

Please note that Psomagen sample collection kits are built to protect the samples from being damaged during transport and to comply with the International Air Transport Association (IATA) regulation. If you are using packaging other than that provided by Psomagen, please make sure to follow the "three layers of packaging" rule to avoid the risk of having the package destroyed by the courier:

  • A primary sample receptacle sealed (collection tube).
  • A leak-proof specimen bag containing absorbent material.
  • An outer packaging that meets the local postal regulations and is labeled as “Exempt Human Specimen.”

For more information please refer to page 187 of IATA Dangerous Goods Regulation.

Additional Shipment Requirements

For saliva, ship at room temperature (overnight shipping is not necessary).

For blood, we recommend using overnight shipping the same day that the blood is collected.

  • Blood can be kept at room temperature for up to 48 hours.
  • We request that blood is refrigerated no longer than two weeks.
  • Please do not freeze blood as deletion/duplication analysis is not supported for frozen or partially frozen blood.

Please ship the specimen in a crush-proof container via FedEx Priority Overnight (in accordance with the FedEx Packaging Guidelines for Clinical Samples.

Our US Shipping Address

Attn: Clinical Laboratory Testing Personnel
Psomagen Inc.
1330 Piccard Drive, Ste 103
Rockville, MD 20850

Test for 15 related genes

Gene List

APC
BMPR1A
CDH1
CTNNA1
EPCAM
KIT
MLH1
MSH2
MSH6
NF1
PDGFRA
PMS2
SMAD4
STK11
TP53
 

Test Methodology and Limitations

DNA sequencing involves the extraction of genomic DNA from specimens collected in approved containers and provided the specimen meets required sample minimum quantity (e.g. volume, weight, etc). This is followed by quantification and qualification to ensure the adequacy of amount and purity for sequencing. Subsequently, whole exome sequencing is conducted on an IlluminaTM short read sequencing (SRS) platform (e.g., NovaSeq X PlusTM) at Psomagen, Inc.’s laboratories (CLIA # 21D2062464, CAP # 8742212).

DNA sequence alignment, variant calling, and variant filtering are performed utilizing the Illumina DRAGENTM bioinformatics pipeline (version 4.2.4.) and various tool sets, which align reads to the human reference genome (GRCh38) and identify single nucleotide variants (SNVs) and small insertions/deletions (InDels). Variant annotations are performed using a pipeline available in Fabric Enterprise. Variant review and interpretation are conducted according to the standards and guidelines set forth by the American College of Medical Genetics and Genomics (Richards S, et al., Genet Med., 2015) by Fabric Clinical Labs (CLIA #45D2281059, CAP # 9619501). Only variants classified as pathogenic or likely pathogenic are reported. The following quality filters are applied to all variants: coverage <40x, allele balance outside 0.3-0.7.

Variants in the following genes are reported: APC, BMPR1A, CDH1, CTNNA1, EPCAM, KIT, MLH1, MSH2, MSH6, NF1, PDGFRA, PMS2, SMAD4, STK11, TP53.

This test is designed to detect single nucleotide variants (SNVs) and small insertions/deletions (InDels). Next-Generation Sequencing (NGS) coverage may vary across the genome, potentially resulting in missed variants in regions with low coverage depth. Some genetic abnormalities may be undetectable with the current version of this test. While the DRAGEN bioinformatics pipeline demonstrates high accuracy for variant calling, there remains a possibility of false positive or false negative results due to variant interpretation which relies on current scientific knowledge and available databases. This may lead to the reclassification of reported variants as new information emerges from ongoing research and is updated in the ACMG guidelines. Furthermore, systematic chemical, computational, or human errors may contribute to false positives or false negatives of DNA variants. For any reported variants, confirmation by orthogonal technology and subsequent consultation with a genetic counselor or qualified healthcare provider can help to establish definitive risk. This result should be considered preliminary until such confirmation has been performed.

Clinical management for this individual should be based on personal and family history, along with other relevant information. If considered relevant to this individual’s clinical presentation and/or family history, targeted testing of appropriate family members of this individual for the reported variants may help to interpret these results. For assistance with the interpretation of these results, healthcare professionals may contact Psomagen directly at (301) 251-1007 or support@psomagen.com.

More Resources

  1. Allemani C, Matsuda T, Di Carlo V, et al.: Global surveillance of trends in cancer survival 2000-14 (CONCORD-3): analysis of individual records for 37 513 025 patients diagnosed with one of 18 cancers from 322 population-based registries in 71 countries. Lancet 391 (10125): 1023-1075, 2018. [PUBMED Abstract]

  2. Sung H, Ferlay J, Siegel RL, et al.: Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J Clin 71 (3): 209-249, 2021. [PUBMED Abstract]

  3. American Cancer Society: Cancer Facts and Figures 2023. American Cancer Society, 2023. Available onlineExit Disclaimer. Last accessed Dec. 15, 2023.

  4. Uson PLS, Kunze KL, Golafshar MA, et al.: Germline Cancer Testing in Unselected Patients with Gastric and Esophageal Cancers: A Multi-center Prospective Study. Dig Dis Sci 67 (11): 5107-5115, 2022. [PUBMED Abstract]

  5. Ku GY, Kemel Y, Maron SB, et al.: Prevalence of Germline Alterations on Targeted Tumor-Normal Sequencing of Esophagogastric Cancer. JAMA Netw Open 4 (7): e2114753, 2021. [PUBMED Abstract]

  6. Møller P, Seppälä TT, Bernstein I, et al.: Cancer risk and survival in path_MMR carriers by gene and gender up to 75 years of age: a report from the Prospective Lynch Syndrome Database. Gut 67 (7): 1306-1316, 2018. [PUBMED Abstract]

  7. Abraham SC, Nobukawa B, Giardiello FM, et al.: Fundic gland polyps in familial adenomatous polyposis: neoplasms with frequent somatic adenomatous polyposis coli gene alterations. Am J Pathol 157 (3): 747-54, 2000. [PUBMED Abstract]

  8. Giardiello FM, Brensinger JD, Tersmette AC, et al.: Very high risk of cancer in familial Peutz-Jeghers syndrome. Gastroenterology 119 (6): 1447-53, 2000. [PUBMED Abstract]

  9. Correa P, Haenszel W, Cuello C, et al.: A model for gastric cancer epidemiology. Lancet 2 (7924): 58-60, 1975. [PUBMED Abstract]

  10. Hooi JKY, Lai WY, Ng WK, et al.: Global Prevalence of Helicobacter pylori Infection: Systematic Review and Meta-Analysis. Gastroenterology 153 (2): 420-429, 2017. [PUBMED Abstract]

  11. Tsugane S, Sasazuki S: Diet and the risk of gastric cancer: review of epidemiological evidence. Gastric Cancer 10 (2): 75-83, 2007. [PUBMED Abstract]

  12. Liu SJ, Huang PD, Xu JM, et al.: Diet and gastric cancer risk: an umbrella review of systematic reviews and meta-analyses of prospective cohort studies. J Cancer Res Clin Oncol 148 (8): 1855-1868, 2022. [PUBMED Abstract]

  13. Song Y, Liu X, Cheng W, et al.: The global, regional and national burden of stomach cancer and its attributable risk factors from 1990 to 2019. Sci Rep 12 (1): 11542, 2022. [PUBMED Abstract]

  14. Shimizu H, Mack TM, Ross RK, et al.: Cancer of the gastrointestinal tract among Japanese and white immigrants in Los Angeles County. J Natl Cancer Inst 78 (2): 223-8, 1987. [PUBMED Abstract]

  15. Mousavi SM, Brandt A, Weires M, et al.: Cancer incidence among Iranian immigrants in Sweden and Iranian residents compared to the native Swedish population. Eur J Cancer 46 (3): 599-605, 2010. [PUBMED Abstract]

  16. Lee J, Demissie K, Lu SE, et al.: Cancer incidence among Korean-American immigrants in the United States and native Koreans in South Korea. Cancer Control 14 (1): 78-85, 2007. [PUBMED Abstract]

  17. Bouras E, Tsilidis KK, Triggi M, et al.: Diet and Risk of Gastric Cancer: An Umbrella Review. Nutrients 14 (9): , 2022. [PUBMED Abstract]

  18. Poly TN, Lin MC, Syed-Abdul S, et al.: Proton Pump Inhibitor Use and Risk of Gastric Cancer: Current Evidence from Epidemiological Studies and Critical Appraisal. Cancers (Basel) 14 (13): , 2022. [PUBMED Abstract]

  19. Shah SC, McKinley M, Gupta S, et al.: Population-Based Analysis of Differences in Gastric Cancer Incidence Among Races and Ethnicities in Individuals Age 50 Years and Older. Gastroenterology 159 (5): 1705-1714.e2, 2020. [PUBMED Abstract]

  20. Anderson WF, Rabkin CS, Turner N, et al.: The Changing Face of Noncardia Gastric Cancer Incidence Among US Non-Hispanic Whites. J Natl Cancer Inst 110 (6): 608-615, 2018. [PUBMED Abstract]

  21. Islami F, DeSantis CE, Jemal A: Incidence Trends of Esophageal and Gastric Cancer Subtypes by Race, Ethnicity, and Age in the United States, 1997-2014. Clin Gastroenterol Hepatol 17 (3): 429-439, 2019. [PUBMED Abstract]

  22. Holowatyj AN, Ulrich CM, Lewis MA: Racial/Ethnic Patterns of Young-Onset Noncardia Gastric Cancer. Cancer Prev Res (Phila) 12 (11): 771-780, 2019. [PUBMED Abstract]

  23. De B, Rhome R, Jairam V, et al.: Gastric adenocarcinoma in young adult patients: patterns of care and survival in the United States. Gastric Cancer 21 (6): 889-899, 2018. [PUBMED Abstract]

  24. Gupta S, Tao L, Murphy JD, et al.: Race/Ethnicity-, Socioeconomic Status-, and Anatomic Subsite-Specific Risks for Gastric Cancer. Gastroenterology 156 (1): 59-62.e4, 2019. [PUBMED Abstract]

  25. Hemminki K, Sundquist J, Ji J: Familial risk for gastric carcinoma: an updated study from Sweden. Br J Cancer 96 (8): 1272-7, 2007. [PUBMED Abstract]

  26. Yaghoobi M, Bijarchi R, Narod SA: Family history and the risk of gastric cancer. Br J Cancer 102 (2): 237-42, 2010. [PUBMED Abstract]

  27. Lissowska J, Groves FD, Sobin LH, et al.: Family history and risk of stomach cancer in Warsaw, Poland. Eur J Cancer Prev 8 (3): 223-7, 1999. [PUBMED Abstract]

  28. Palli D, Russo A, Ottini L, et al.: Red meat, family history, and increased risk of gastric cancer with microsatellite instability. Cancer Res 61 (14): 5415-9, 2001. [PUBMED Abstract]

Our Certifications

CLIA ID number: 21D2062464
CAP ID number: 8742212