Lynch syndrome

Lynch syndrome, previously known as hereditary non-polyposis colorectal cancer (HNPCC), is caused by mutations in the mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, and EPCAM. Lynch syndrome is the most common hereditary form of colorectal cancer. It affects about 1 in 440 individuals in the U.S.

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Test Code: 4646 Test Name: PMS2 seq and del/dup TAT 14-21 days Gene: 1
Test Code: 8508 Test Name: MLH1 seq and del/dup TAT 14-21 days Gene: 1
Test Code: 8510 Test Name: MSH2 seq & del/dup & EPCAM del/dup TAT 14-21 days Genes: 2
Test Code: 8512 Test Name: MSH6 seq and del/dup TAT 14-21 days Gene: 1
Test Code: 8515 Test Name: HNPCC/Lynch seq and del/dup TAT 2-6 weeks Genes: 5
Test Code: 8517 Test Name: HNPCC concurrent TAT 14-21 days Genes: 5

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Test Description

MLH1 coding exons 1-19, MSH2 coding exons 1-16, MSH6 coding exons 1-10, and PMS2 coding exons 1-15, and well into the 5’ and 3’ ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for all coding exons of MLH1, MSH2, MSH6, and PMS2, and coding exon 9 of EPCAM. The inversion of coding exons 1-7 of the MSH2 gene is detected by NGS and confirmed by PCR and agarose gel electrophoresis. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology, using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.Gross deletion/duplication analysis of MLH1, MSH2, MSH6, and PMS2 using read-depth from NGS data and EPCAM using multiplex ligation-dependent probe amplification (MLPA) is also performed. Any copy number changes detected by NGS are confirmed by targeted chromosomal microarray and/or MLPA.  If a deletion is detected in exons 13, 14, or 15 of PMS2, double stranded sequencing of the appropriate exon(s) of the pseudogene, PMS2CL, will be performed to determine if the deletion is located in the PMS2 gene or pseudogene. If a deletion is detected in exon 9 of EPCAM, deletion/duplication analysis of coding exons 3 and 8 of EPCAM will be performed. For EPCAM, only gross deletions encompassing the 3’ end of the gene are reported.

 

1. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.

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