Targeted next‐generation sequencing of 22 mismatch repair genes identifies Lynch syndrome families

Causative germline mutations in mismatch repair ( MMR ) genes can only be identified in ~50% of families with a clinical diagnosis of the inherited colorectal cancer ( CRC ) syndrome hereditary nonpolyposis colorectal cancer ( HNPCC )/Lynch syndrome ( LS ). Identification of these patients are critical as they are at substantially increased risk of developing multiple primary tumors, mainly colorectal and endometrial cancer ( EC ), occurring at a young age. This demonstrates the need to develop new and/or more thorough mutation detection approaches. Next‐generation sequencing ( NGS ) was used to screen 22 genes involved in the DNA MMR pathway in constitutional DNA from 14 HNPCC and 12 sporadic EC patients, plus 2 positive controls. Several softwares were used for analysis and functional annotation. We identified 5 exonic indel variants, 42 exonic nonsynonymous single‐nucleotide variants ( SNV s) and 1 intronic variant of significance. Three of these variants were class 5 (pathogenic) or class 4 (likely pathogenic), 5 were class 3 (uncertain clinical relevance) and 40 were classified as variants of unknown clinical significance. In conclusion, we have identified two LS families from the sporadic EC patients, one without a family history of cancer, supporting the notion for universal MMR screening of EC patients. In addition, we have detected three novel class 3 variants in EC cases. We have, in addition discovered a polygenic interaction which is the most likely cause of cancer development in a HNPCC patient that could explain previous inconsistent results reported on an intronic EXO 1 variant.