title: Genetic variants of the DNA repair genes from Exome Aggregation Consortium (EXAC) database: significance in cancer.
abstract: DNA repair pathway is a primary defense system that eliminates wide varieties of DNA damage. Any deficiencies in them are likely to cause the chromosomal instability that leads to cell malfunctioning and tumorigenesis. Genetic polymorphisms in DNA repair genes have demonstrated a significant association with cancer risk. Our study attempts to give a glimpse of the overall scenario of the germline polymorphisms in the DNA repair genes by taking into account of the Exome Aggregation Consortium (ExAC) database as well as the Human Gene Mutation Database (HGMD) for evaluating the disease link, particularly in cancer. It has been found that ExAC DNA repair dataset (which consists of 228 DNA repair genes) comprises 30.4% missense, 12.5% dbSNP reported and 3.2% ClinVar significant variants. 27% of all the missense variants has the deleterious SIFT score of 0.00 and 6% variants carrying the most damaging Polyphen-2 score of 1.00, thus affecting the protein structure and function. However, as per HGMD, only a fraction (1.2%) of ExAC DNA repair variants was found to be cancer-related, indicating remaining variants reported in both the databases to be further analyzed. This, in turn, may provide an increased spectrum of the reported cancer linked variants in the DNA repair genes present in ExAC database. Moreover, further in silico functional assay of the identified vital cancer-associated variants, which is essential to get their actual biological significance, may shed some lights in the field of targeted drug development in near future.
authors.affiliation: Department of Biotechnology Assam University, Silchar, 788011, Assam, India.
authors.forename: Raima
authors.initials: R
authors.lastname: Das
authors.affiliation: Department of Biotechnology Assam University, Silchar, 788011, Assam, India; University of Kalyani, Nadia, 741235, West Bengal, India. Electronic address: drsankarghosh@gmail.com.
authors.forename: Sankar Kumar
authors.initials: SK
authors.lastname: Ghosh
mesh_terms: D004260:DNA Repair; D030561:Databases, Nucleic Acid; D059472:Exome; D005796:Genes; D020022:Genetic Predisposition to Disease; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism*; D011110:Polymorphism, Genetic
keywords: Cancer; DNA repair; DNA repair variants status; ExAC database; Germline variants; HGMD