Genome‐wide CNV analysis in 221 unrelated patients and targeted high‐throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis

Abstract

To uncover novel causative genes in patients with unexplained adenomatous polyposis, a model disease for colorectal cancer, we performed a genome-wide analysis of germline copy number variants (CNV) in a large, well characterized APC and MUTYH mutation negative patient cohort followed by a targeted next generation sequencing (NGS) approach. Genomic DNA from 221 unrelated German patients was genotyped on high-resolution SNP arrays. Putative CNVs were filtered according to stringent criteria, compared with those of 531 population-based German controls, and validated by qPCR. Candidate genes were prioritized using in silico, expression, and segregation analyses, data mining and enrichment analyses of genes and pathways. In 27% of the 221 unrelated patients, a total of 77 protein coding genes displayed rare, nonrecurrent, germline CNVs. The set included 26 candidates with molecular and cellular functions related to tumorigenesis. Targeted high-throughput sequencing found truncating point mutations in 12% (10/77) of the prioritized genes. No clear evidence was found for autosomal recessive subtypes. Six patients had potentially causative mutations in more than one of the 26 genes. Combined with data from recent studies of early-onset colorectal and breast cancer, recurrent potential loss-of-function alterations were detected in CNTN6, FOCAD (KIAA1797), HSPH1, KIF26B, MCM3AP, YBEY and in three genes from the ARHGAP family. In the canonical Wnt pathway oncogene CTNNB1 (b-catenin), two potential gain-of-function mutations were found. In conclusion, the present study identified a group of rarely affected genes which are likely to predispose to colorectal adenoma formation and confirmed previously published candidates for tumor predisposition as etiologically relevant.Germline copy number variants (CNVs) have been recognized as the most prevalent type of structural genetic variation, which also predispose to human disease as lowpenetrance risk factors or high-penetrance mutations. 1,2 Recent research has identified potentially causative germline deletions and duplications for a number of sporadic and familial types of cancer. [3][4][5][6][7] In hereditary cancer syndromes, heterozygous microdeletions of single exons or whole genes contribute substantially to the mutation spectrum. 8,9 A plausible hypothesis therefore is that in particular deletion CNVs are part of the mutation spectrum of yet unidentified genes responsible for monogenic tumor syndromes for which no causative germline mutation in established genes has yet been identified.

Exome Sequencing Identifies Biallelic MSH3 Germline Mutations as a Recessive Subtype of Colorectal Adenomatous Polyposis

“…9 In addition, a single nucleotide polymorphism (SNP) array-based CNV analysis was performed in all individuals, as described elsewhere. 28 …”

“…Finally, all genes carrying the remaining rare variants were inspected for the presence of rare, non-polymorphic heterozygous CNVs of ≥ 10 kb in order to identify additional recurrently mutated genes or biallelic, compound-heterozygous variants. 28 …”

“…23-26 In addition, rare germline copy number variants (CNV) and low-penetrant variants might contribute to the genetic predisposition for formation of colorectal adenomas. 15; 27; 28 …”

Gastric cancer and gene copy number variation: emerging cancer drivers for targeted therapy

“…12 DNA CNVs include gene amplification, gain, loss and deletion. In addition to gene mutation, CNV has a significant role in tumorigenesis in many cancers, such as GC, 13 ovarian cancer, 14 hepatocellular carcinoma, 15 testicular germ cell tumors, 16 colorectal carcinoma, 17 bladder cancer 18 and so on. The accumulation of CNVs during gastric oncogenesis may be a result of preferential selection by which transforming cells gain evolutionary advantage.…”

Genome-wide association study identified copy number variants associated with sporadic colorectal cancer risk

“…Interestingly, a recent study identified germline mutation in SMARCA4 , another member of the SNF/SW1 superfamily, in several polyposis families,17 suggesting that members of chromatin remodellers are important regulators of tumourigenesis process. We investigated the expression of the H1 binding domain of CHD8 ( CHD8H1 ) in a subset of cases but found that the expression did not follow their CN status in both mucosa and tumours normalised to their matched mucosa.…”