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HNPCC/Lynch Syndrome (MSH2) Sequencing and Deletion/Duplication
0051654
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.

Mnemonic
MSH2 FGA
Methodology
Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification
Performed
Varies
Reported
28-35 days
New York DOH Approval Status
This test is New York DOH approved.
Specimen Required
Patient Preparation
 
Collect
Lavender (EDTA), pink (K2EDTA), or yellow (ACD solution A or B). 
Specimen Preparation
Transport 3 mL whole blood. (Min: 2 mL) 
Storage/Transport Temperature
Refrigerated. 
Unacceptable Conditions
 
Remarks
 
Stability
Ambient: 72 hours; Refrigerated: 1 week; Frozen: Unacceptable 
Reference Interval
Available Separately
Components
Reference Interval
NoMSH2 Full Gene SequencingBy report
NoMSH2 Deletion/Duplication/InversionBy 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.
Incidence:
1-2 percent of colorectal cancer is due to pathogenic mismatch repair gene variants.
Inheritance:
Autosomal dominant.
Penetrance:
80 percent lifetime risk of colorectal cancer; 20-60 percent risk for endometrial cancer.
Cause:
Pathogenic germline MLH1, MSH2, MSH6, and PMS2 gene variants.
Gene tested:
MSH2
Clinical Sensitivity:
40 percent of Lynch syndrome is due to pathogenic MSH2 variants.
Methodology:
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.

Compliance Statement C: For human genetic inheritable conditions and mutations. This test was developed and its performance characteristics determined by ARUP Laboratories. The U. S. Food and Drug Administration has not approved or cleared this test; however, FDA clearance or approval is not currently required for clinical use. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions.

Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Note
Hotline History
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Components
Component Test Code*Component Chart NameLOINC
0051653MSH2 Full Gene Analysis
2001367MSH2 FGA Specimen
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Aliases
  • HNPCC
  • MSH2 gene testing
  • MSH2 genotyping
  • MSH2 germline mutation assay