HNPCC/Lynch Syndrome (MSH2) Sequencing and Deletion/Duplication
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.

Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification
28-35 days
New York DOH Approval Status
This test is New York DOH approved.
ARUP Consult®
Disease Topics
Specimen Required
Patient Preparation
Lavender (EDTA), 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: 72 hours; Refrigerated: 1 week; Frozen: Unacceptable 
Reference Interval
Available SeparatelyComponentsReference Interval
NoMSH2 Full Gene SequencingBy report
NoMSH2 DeletionsBy report

Interpretive Data
Background Information for HNPCC/Lynch syndrome (MSH2) Sequencing and Deletion/Duplication:
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 mismatch repair gene mutations.
Autosomal dominant
80 percent lifetime risk of colorectal cancer; 20-60 percent risk for endometrial cancer.
Pathogenic Germline MLH1, MSH2, MSH6, and PMS2 gene mutations.
Gene tested: MSH2
Clinical Sensitivity:
40 percent of Lynch syndrome cases are due to MSH2 mutations
Methodology: Bidirectional sequencing of MSH2 coding regions and intron-exon boundaries; multiplex ligation-dependent probe amplification (MLPA) to detect large MSH2 exonic deletions and EPCAM (TACSTD1) exon 9 deletions.
Analytical Sensitivity & Specificity: 99 percent.
Test Limitations:
Diagnostic errors can occur due to rare sequence variations. The breakpoints of large deletions/duplications will not be determined. Regulatory region mutations, deep intronic mutations and mutations in genes other than MSH2 will not be detected.

This test is performed pursuant to an agreement with Roche Molecular Systems, Inc.

Compliance Statement C: The performance characteristics of this test were validated by ARUP Laboratories. The U.S. Food and Drug Administration (FDA) has not approved or cleared this test. However, FDA approval or clearance is currently not required for clinical use of this test. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions. ARUP is authorized under Clinical Laboratory Improvement Amendments (CLIA) and by all states to perform high-complexity testing. Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Component Test Code*Component Chart NameLOINC
0051653MSH2 Full Gene Analysis
2001367MSH2 FGA Specimen
* 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