Integrated Analysis of Germline and Tumor DNA Identifies New Candidate Genes Involved in Familial Colorectal Cancer

Abstract

Colorectal cancer (CRC) shows aggregation in some families but no alterations in the known hereditary CRC genes. We aimed to identify new candidate genes which are potentially involved in germline predisposition to familial CRC. An integrated analysis of germline and tumor whole-exome sequencing data was performed in 18 unrelated CRC families. Deleterious single nucleotide variants (SNV), short insertions and deletions (indels), copy number variants (CNVs) and loss of heterozygosity (LOH) were assessed as candidates for first germline or second somatic hits. Candidate tumor suppressor genes were selected when alterations were detected in both germline and somatic DNA, fulfilling Knudson’s two-hit hypothesis. Somatic mutational profiling and signature analysis were also performed. A series of germline-somatic variant pairs were detected. In all cases, the first hit was presented as a rare SNV/indel, whereas the second hit was either a different SNV (3 genes) or LOH affecting the same gene (141 genes). BRCA2, BLM, ERCC2, RECQL, REV3L and RIF1 were among the most promising candidate genes for germline CRC predisposition. The identification of new candidate genes involved in familial CRC could be achieved by our integrated analysis. Further functional studies and replication in additional cohorts are required to confirm the selected candidates.

Germline biallelic Mcm8 variants are associated with early-onset Lynch-like syndrome

“…Sequencing data analysis. The GATK HaplotypeCaller tool was used for single nucleotide variants (SNVs) and short indels calling in germline samples, and GATK MuTect2 and Strelka2 were applied in tumor samples using previously developed R language in-house pipelines (29)(30)(31)(32). Several databases were evaluated for variant annotation, including SnpEff and dbNSFP.…”

Dominantly Inherited Hereditary Nonpolyposis Colorectal Cancer Not Caused by MMR Genes

“…Nucleotide excision repair (NER) is mainly involved in the removal of bulky adducts that results from UV DNA damage. While biallelic mutations in the main NER genes are linked to xeroderma pigmentosum, heterozygous likely pathogenic missense variants in XPC , ERCC2 , and ERCC6 have been identified in CRC patients [ 12 , 32 , 33 ]. Additional studies will determine whether the identified variants are or are not causally associated with an increased CRC risk.…”

“…RIF1 encodes a protein that localizes to aberrant telomeres and is recruited to DSBs to counteract DNA resection, thus promoting repair by NHEJ. The authors identified a predicted pathogenic RIF1 missense variant and tumor LOH in the proband of one of the studied CRC families [ 33 ]. As no additional evidence has been reported, we looked up RIF1 in the exome sequencing data reported by Chubb et al (2016).…”

Candidate Gene Discovery in Hereditary Colorectal Cancer and Polyposis Syndromes–Considerations for Future Studies

“…We reviewed these studies following the general setup of candidate discovery studies, which cover cohort composition, variant discovery and prioritization, and variant validation ( Table 1 , Table S1 ). Six studies based discovery on the same cohort that was enlarged over time [ 53 , 64 , 69 , 72 , 75 , 76 ].…”

“…We noted that among the 37 candidate gene discovery studies, FH-based inclusion criteria varied from study to study. Some studies used a relatively broad inclusion criterion such as “one first-degree relative or second-degree relative with CRC” while others applied more stringent criteria “the presence of at least three relatives with CRC, of which at least two in consecutive affected generations and at least one case diagnosed with CRC before the age of 60” ( Table 1 : Inclusion criteria FH) [ 42 , 43 , 48 , 50 , 53 , 56 , 59 , 64 , 69 , 70 , 72 , 75 , 76 ]. Furthermore, phenotypic characteristics strongly associated with hereditary CRC and polyposis syndromes, such as tumor types and age-of-onset strongly varied between, but also within cohorts ( Table 1 : Inclusion criteria index phenotype; Table 1 : Inclusion criteria age).…”