All coding exons (plus 15 bp upstream and downstream of each coding exon) of the targeted gene(s) are captured, sequenced using NGS and aligned to the human reference genome. A minimum NGS coverage of 20X is achieved for all coding exons +/- 5 bp, and a minimum coverage of 10X an additional 10 bp from +/- 6 bp through +/- 15 bp. A minimum coverage of 10X is achieved for all clinically significant promoter regions. Regions which do not meet these coverage metrics are filled with targeted Sanger Sequencing. Variants in the targeted regions that are of potential clinical significance, based on the ACMG guidelines for interpretation of sequence variants (PMID: 25741868), will be reported. Copy number variation is assessed by coverage depth within the targeted regions compared to a normalized reference file. Copy number variants within the targeted regions that are of potential clinical significance will also be reported. In addition to NGS, Sanger sequencing is used to amplify and sequence MLH1 and MSH2 promoter regions and PMS2 to avoid known pseudogene regions. All reported variants of potential clinical significance not meeting the sequencing quality criteria will be confirmed by a different technology.
Targeted NGS MLH1, MSH2, MSH6, and PMS2 sequencing and deletion/duplication analysis is used for the detection of germline pathogenic variants in patients at increased risk for hereditary colorectal cancer and cancers of the endometrium, stomach, ovary, small bowel, hepatobiliary tract, urinary tract, brain, and skin. Not all individuals with pathogenic MLH1, MSH2, MSH6, or PMS2 variants will have hereditary colorectal cancer. Patients with such pathogenic variants face an estimated 52-82% for colorectal cancer; 25-60% for endometrial cancer in women; 6-13% for gastric cancer; and 4-12% for ovarian cancer. Other types of cancers have also been reported in individuals with pathogenic MLH1, MSH2, MSH6, or PMS2 variants (https://www.ncbi.nlm.nih.gov/books/NBK1211/).
Interpretive report provided
* Reference ranges may change over time. Please refer to the original patient report when evaluating results.
This assay will not detect intronic variants or copy number variants outside the region sequenced in the MLH1, MSH2, MSH6, PMS2 genes or variants in other genes associated with these diseases will not be identified.
Collect specimen in a lavender top tube. Send intact specimen within 24 hours if stored at room temperature or within 5 days if stored refrigerated. Include the patient's family history, pedigree, and ethnicity on the test requisition. Obtaining informed consent from the patient prior to genetic testing is strongly recommended. If desired, a UMHS Request and Consent for Genetic Testing form can be obtained from the MMGL Molecular Genetics Laboratory by contacting the MLabs Client Services Center at 800-862-7284 or online at https://mlabs.umich.edu/media/188.
Most insurance carriers require prior authorization for payment. MLH1, MSH2, MSH6, and PMS2 testing will not begin until insurance prior authorization is received by the MMGL Laboratory or it has been confirmed that prior authorization is not required. It is the obligation of the ordering health care provider to obtain prior authorization before testing can begin. To obtain BCN prior authorization call Joint Venture Hospital Laboratories (JVHL) at 800-445-4979; for all others insurances, contact the plan directly. By ordering this test the clinician acknowledges that informed consent has been obtained from the patient as required by applicable state or federal laws and the ordering clinician has authorization from the patient permitting MLabs to report the test results to the ordering clinician. Test includes medical geneticist interpretation of results billed as a separate additional charge. This test is not available without interpretation.