Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes

In many families with suspected Lynch syndrome(LS), no germline mutationin the causative mismatch repair (MMR) genes is detected during routine diagnostics. To identify novel causative genes for LS, the present study investigated 77 unrelated, mutation-negative patients with clinically suspected LS and a loss of MSH2in tumor tissue. An analysis for genomic copy number variants (CNV) was performed, with subsequent next generation sequencing (NGS) of selected candidate genesin a subgroup of the cohort. Genomic DNA was genotyped using Illumina's HumanOmniExpress Bead Array. After quality control and filtering, 25 deletions and 16 duplications encompassing 73 genes were identified in 28 patients. No recurrent CNV was detected, and none of the CNVs affected the regulatory regions of MSH2. A total of 49 candidate genesfrom genomic regions implicated by the present CNV analysis and 30 known or assumed risk genes for colorectal cancer (CRC) were then sequenced in a subset of 38 patients using a customized NGS gene panel and Sanger sequencing. Single nucleotide variants were identified in 14 candidate genesfrom the CNV analysis. The most promising of these candidate geneswere: (i) PRKCA, PRKDC, and MCM4, as a functional relation to MSH2is predicted by network analysis, and (ii) CSMD1, as this is commonly mutated in CRC. Furthermore, six patients harbored POLE variants outside the exonucleasedomain, suggesting that these might be implicated in hereditary CRC. Analyses in larger cohorts of suspected LS patients recruitedvia international collaborations are warranted to verify the present findings.