Ordering Recommendation

Detect germline MSH2 variants. Use in MMR-deficient carcinoma with suggestive IHC results (loss of MSH2 and MSH6 proteins). Includes evaluation of EPCAM exon 9 deletions and 10 Mb inversion of MSH2 exons 1-7.




Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification




28-35 days

New York DOH Approval Status

This test is New York DOH approved.

Specimen Required

Patient Preparation

Lavender (K2EDTA), Pink (K2EDTA), or Yellow (ACD Solution A or B).

Specimen Preparation

Transport 3 mL whole blood. (Min: 2 mL)

Storage/Transport Temperature


Unacceptable Conditions

Ambient: 1 week; Refrigerated: 1 month; Frozen: 6 months

Reference Interval

Available Separately
Reference Interval
No MSH2 Full Gene Sequencing By report
No MSH2 Deletion/Duplication/Inversion By report

Interpretive Data

Background Information for HNPCC/Lynch syndrome (MSH2) 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.
1-2 percent of colorectal cancer is due to pathogenic mismatch repair gene variants.
Autosomal dominant.
80 percent lifetime risk of colorectal cancer; 20-60 percent risk for endometrial cancer.
Pathogenic germline MLH1, MSH2, MSH6, and PMS2 gene variants.
Gene tested:
Clinical Sensitivity: 40 percent of Lynch syndrome is due to pathogenic MSH2 variants.
Bidirectional sequencing of MSH2 coding regions and intron-exon boundaries; multiplex ligation-dependent probe amplification (MLPA) to detect large exonic deletions and duplications of MSH2, EPCAM (TACSTD1) exon 9 and the 10Mb MSH2 exons1-7 inversion.
Analytical Sensitivity & Specificity:
99 percent.
Test Limitations:
Diagnostic errors can occur due to rare sequence variations. The breakpoints of large deletions/duplications/inversions will not be determined. Deep intronic and regulatory region variants will not be detected. Variants in genes other than MSH2 and TACSTD1, as described above, will not be detected. 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.

Compliance Category

Laboratory Developed Test (LDT)


Hotline History


CPT Codes

81295; 81297


Component Test Code* Component Chart Name LOINC
0051653 MSH2 Full Gene Analysis 79415-6
2001367 MSH2 FGA Specimen 66746-9
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.


  • MSH2 gene testing
  • MSH2 genotyping
  • MSH2 germline mutation assay
HNPCC/Lynch Syndrome (MSH2) Sequencing and Deletion/Duplication (INACTIVE as of 11/15/21)