HNPCC/Lynch Syndrome (MLH1) Sequencing and Deletion/Duplication (INACTIVE as of 11/15/21)
Detect germline MLH1 variants. Use in MMR-deficient carcinoma with suggestive IHC results (loss of MLH1 and PMS2 proteins), negative for the BRAF codon 600 pathogenic variant, and normal MLH1 methylation studies.
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
|No||MLH1 Sequencing||By report|
|No||MLHI Deletion/Duplication||By report|
Background Information for HNPCC/Lynch Syndrome (MLH1) Sequencing and Deletion/Duplication:
Characteristics: 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 of MLH1 Mutations: 80 percent lifetime risk of colorectal cancer; 20-60 percent risk for endometrial cancer.
Cause: Pathogenic germline MLH1, MSH2, MSH6, and PMS2 gene mutations.
Gene Tested: MLH1
Clinical Sensitivity: Approximately 45 percent of Lynch syndrome is due to MLH1 mutations.
Methodology: Bidirectional sequencing of MLH1 coding regions and intron-exon boundaries; multiplex ligation-dependent probe amplification (MLPA) to detect large MLH1 exonic deletions.Analytical Sensitivity & Specificity: 99 percent.
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 MLH1 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.
Laboratory Developed Test (LDT)
|Component Test Code*||Component Chart Name||LOINC|
|0051651||Lynch Syndrome (MLH1) Interpretation||79416-4|
|2001365||MLH1 FGA Specimen||66746-9|
- MLH1gene testing
- MLH1 genotyping
- MLH1 Full Gene Analysis
- MLH1 Hypermethylation
- MLH1germline assay