HNPCC/Lynch Syndrome (PMS2) Sequencing and Deletion/Duplication (INACTIVE as of 11/15/21)
Detect germline PMS2 variants. Use in MMR-deficient carcinoma with suggestive IHC results (isolated loss of PMS2 protein).
Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification
New York DOH Approval Status
Lavender (K2EDTA), Pink (K2EDTA), or Yellow (ACD Solution A or B).
Transport 3 mL whole blood. (Min: 1 mL)
Ambient: 1 week; Refrigerated: 1 month; Frozen: 6 months
Background information for HNPCC/Lynch Syndrome (PMS2) Sequencing and Deletion/Duplication
Characteristics of Lynch Syndrome: Increased risk of colorectal and extra-colonic cancers including endometrial, renal pelvis, ureter, ovary, stomach, small intestine and hepatobiliary tract.
Incidence: 1-2 percent of colorectal cancer is due to mismatch repair gene mutations.
Inheritance: Autosomal dominant.
Penetrance: Unknown for PMS2 mutations.
Cause: Pathogenic germline MLH1, MSH2, MSH6, and PMS2 gene mutations.
Gene tested: PMS2
Clinical Sensitivity: Less than 5 percent of Lynch syndrome cases are due to PMS2 mutations.
Methodology: Bidirectional sequencing of PMS2 coding regions and intron-exon boundaries; multiplex ligation-dependent probe amplification (MLPA) to detect large PMS2 exonic deletions.
Analytical Sensitivity & Specificity: 99 percent.
Limitations: Diagnostic errors can occur due to rare sequence variations. Regulatory region mutations and deep intronic mutations will not be detected. Mutations in genes other than PMS2 are not evaluated. This assay is not designed to detect somatic variants associated with malignancy. Interpretation of this test result may be impacted if the patient has had an allogeneic stem cell transplantation.
This test was developed and its performance characteristics determined by ARUP Laboratories. It has not been cleared or approved by the US Food and Drug Administration. This test was performed in a CLIA certified laboratory and is intended for clinical purposes.
Counseling and informed consent are recommended for genetic testing. Consent forms are available online.
Laboratory Developed Test (LDT)
Suspected deletions or duplications in exons 12-15 require additional sequencing to exclude pseudogene copy number variants. Additional charges apply.
81317; 81319; If pseudogene analysis is performed add: 81479
|Component Test Code*||Component Chart Name||LOINC|
|0051738||Lynch Syndrome (PMS2) Interpretation||79417-2|
|2001372||PMS2 FGA Specimen||66746-9|
- PMS2 gene testing
- PMS2 genotyping
- PMS2 germline assay