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

Abstract

In many families with suspected Lynch syndrome (LS), no germline mutation in 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 MSH2 in tumor tissue. An analysis for genomic copy number variants (CNV) was performed, with subsequent next generation sequencing (NGS) of selected candidate genes in 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 genes from 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 genes from the CNV analysis. The most promising of these candidate genes were: (i) PRKCA, PRKDC, and MCM4, as a functional relation to MSH2 is predicted by network analysis, and (ii) CSMD1, as this is commonly mutated in CRC. Furthermore, six patients harbored POLE variants outside the exonuclease domain, suggesting that these might be implicated in hereditary CRC. Analyses in larger cohorts of suspected LS patients recruited via international collaborations are warranted to verify the present findings.

From colorectal cancer pattern to the characterization of individuals at risk: Picture for genetic research in Latin America

“…Our data support the recommendation on the application of population‐based screening protocols for all CRC and endometrial cancers diagnosed below age 70 using IHC of the MMR proteins . Nonetheless, patients with a young age of onset and/or a positive family history of LS‐associated cancers without an identified path_MMR variant, may suggest the involvement of pathogenic variants in as yet undiscovered genes …”

Deregulation of CSMD1 targeted by microRNA-10b drives gastric cancer progression through the NF-κB pathway

“…Multiple mechanisms can reduce the expression of CSMD1. The allelic loss, copy number aberrations, mutations, and methylations of CSMD1 have been detected in various malignant tumours such as head and neck tumor, colorectal cancers, liver cancer, and so on [5][6][7][8][9][10][11][12][13][14][15][16]. Besides, it has been proved that the change of microRNA expression and dysfunction play an important role in tumorigenesis and metastasis by regulating target genes and pathways, subsequently resulting in the alteration of proliferation, differentiation, apoptosis, invasion and metastasis of tumor cells [17][18][19].…”

Population‐wide copy number variation calling using variant call format files from 6,898 individuals

“…Whole-genome sequencing (WGS) at high depth has been the gold standard for detecting large polymorphisms in population studies and is starting to replace array-based calling in the clinic. Such methods were pioneered in the era of genotyping chips (PennCNV; Wang et al, 2007) and PlatinumCNV (Kumasaka et al, 2011), are still widely used (Kayser et al, 2018;Selvanayagam et al, 2018) and have recently been proposed to call CNVs from markerlevel data in paired cancer samples (Putnam et al, 2017). The reasons for this are two-fold.…”