Lynch Syndrome via the PMS2 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
7507 PMS2 81317 81317,81319 $540 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7507PMS281317 81317(x1), 81319(x1) $540 Order Options and Pricing

Pricing Comments

This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Lynch syndrome (OMIM 120435), also called hereditary nonpolyposis colorectal cancer (HNPCC), is an inherited cancer syndrome caused by germline variants in DNA mismatch repair (MMR) genes. MMR genes are responsible for repairing small sequence errors, or mismatches, during DNA replication. Variants in a single mismatch repair gene can cause widespread genomic instability characterized by the expansion or contraction of short tandem repeat sequences (or microsatellites) (reviewed by Grady and Carethers in Gastroenterology 135:1079-1099, 2008). This phenomenon of microsatellite instability (MSI) leads to somatic variants in oncogenes or tumor suppressor genes, including TGFBR2 and NF1 among others (Wang et al. Hum Genet 112:117-123, 2003). As a result, Lynch syndrome is marked by early onset and high lifetime risk of cancer, particularly in the right colon but also in the endometrium, ovary, stomach, bile duct, kidney, bladder, ureter, and brain (Jang and Chung Gut and Liver 4:151-160, 2010). Clinical hallmarks of Lynch syndrome, as delineated by the Amsterdam criteria, include heritable colorectal (type I) or extracolonic (type II) cancer, present in at least three relatives over at least two consecutive generations, with an onset of cancer before the age of 50 in at least one case, and pathological MSI within tumors (Vasen et al. Gastroenterology 116:1453-1456, 1999).

Genetics

Lynch syndrome is an autosomal dominant disease caused by germline variants in one of six described MMR genes: MLH1, MSH2, MSH6, MLH3, PMS1, and PMS2 (Peltomaki and Vasen Dis Markers 20:269-276, 2004). Variants in MLH1 and MSH2 account for 80-90% of all Lynch patients and most frequently occur in families meeting the stringent Amsterdam I criteria. Variants in MSH6, MLH3, PMS1, and PMS2 account for the remaining Lynch patients and are often found in families with atypical HPNCC symptoms, such as low rates of MSI or extracolonic carcinomas. To date, ~100 pathogenic variations have been reported in the PMS2 gene (OMIM 600258; Human Gene Mutation Database, www.hgmd.cf.ac.uk). While heterozygous germline variants in PMS2 are known to cause Lynch syndrome, biallelic germline PMS2 variants have been identified in patients with constitutive mismatch repair deficiency (CMMR-D) (Wimmer and Etzler Hum Genet 124:105-122, 2008). CMMR-D is characterized by childhood malignancies, mainly hematological and/or neurological, and neurofibromatosis-like café au lait spots.

Clinical Sensitivity - Sequencing with CNV PG-Select

A variant in PMS2 is detected in 1-2% of Lynch patients (Peltomaki et al. Dis Markers 20:269-276, 2004) and ~50% of CMMR-D patients (Wimmer and Etzler Hum Genet 124:105-122, 2008).

Testing Strategy

This test provides full coverage of all coding exons of the PMS2 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are patients with Lynch syndrome or CMMR-D, and relatives of patients with a verified PMS2 variant. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in PMS2. This test is specifically designed for heritable germline variants and is not appropriate for the detection of somatic variants in tumor tissue.

Gene

Official Gene Symbol OMIM ID
PMS2 600259
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Hereditary Nonpolyposis Colorectal Cancer Type 4 614337

Related Tests

Name
Hereditary Breast and Ovarian Cancer - High Risk and Lynch Syndrome Panel
Hereditary Endometrial Cancer Panel
Lynch Syndrome via the EPCAM Gene

Citations

  • Grady WM, Carethers JM. 2008. Genomic and Epigenetic Instability in Colorectal Cancer Pathogenesis. Gastroenterology 135: 1079–1099. PubMed ID: 18773902
  • Human Gene Mutation Database.
  • Jang E, Chung DC. 2010. Hereditary Colon Cancer: Lynch Syndrome. Gut and Liver 4: 151. PubMed ID: 20559516
  • Peltomäki P, Vasen H. 2004. Mutations associated with HNPCC predisposition–Update of ICG-HNPCC/INSiGHT mutation database. Disease markers 20: 269–276. PubMed ID: 15528792
  • Vasen HF, Watson P, Mecklin J-P, Lynch HT. 1999. New clinical criteria for hereditary nonpolyposis colorectal cancer (HNPCC, Lynch syndrome) proposed by the International Collaborative group on HNPCC. Gastroenterology 116: 1453–1456. PubMed ID: 10348829
  • Wang Q, Montmain G, Ruano E, Upadhyaya M, Dudley S, Liskay MR, Thibodeau SN, Puisieux A. 2003. Neurofibromatosis type 1 gene as a mutational target in a mismatch repair-deficient cell type. Human genetics 112: 117–123. PubMed ID: 12522551
  • Wimmer K, Etzler J. 2008. Constitutional mismatch repair-deficiency syndrome: have we so far seen only the tip of an iceberg? Human Genetics 124: 105–122. PubMed ID: 18709565

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
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