Contents lists available at ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene Research paper Exploring the deleterious SNPs in XRCC4 gene using computational approach and studying their association with breast cancer in the population of West India Preety K. Singh a , Kinnari N. Mistry a, ⁎ , Haritha Chiramana b , Dharamshi N. Rank c , Chaitanya G. Joshi d a Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidyanagar, Affiliated to Sardar Patel University, Anand, Gujarat 388121, India b Manibhai Shivabhai Patel Cancer Centre, Shree Krishna Hospital, Karamsad, Anand, Gujarat, India c Department of Animal Breeding and Genetics, Anand Agriculture University, Anand, Gujarat, India d Department of Animal Biotechnology, Anand Agriculture University, Anand, Gujarat, India ARTICLE INFO Keywords: DNA repair Variant Breast cancer Damaging SNPs ABSTRACT Non-homologous end joining (NHEJ) pathway has pivotal role in repair of double-strand DNA breaks that may lead to carcinogenesis. XRCC4 is one of the essential proteins of this pathway and single-nucleotide poly- morphisms (SNPs) of this gene are reported to be associated with cancer risks. In our study, we first used computational approaches to predict the damaging variants of XRCC4 gene. Tools predicted rs79561451 (S110P) nsSNP as the most deleterious SNP. Along with this SNP, we analysed other two SNPs (rs3734091 and rs6869366) to study their association with breast cancer in population of West India. Variant rs3734091 was found to be significantly associated with breast cancer while rs6869366 variant did not show any association. These SNPs may influence the susceptibility of individuals to breast cancer in this population. 1. Introduction Breast cancer is the most frequently occurring cancer among women worldwide and it is the leading female cancer and cause of death in India, with approximately 75,000 deaths annually (Parkin et al., 2005; Indian Council of Medical Research, 2010). The DNA repair system maintains genomic integrity of mammalian cells. Decrease in DNA re- pair capacity leads to high oxidative stress, which can further initiate carcinogenesis (Oldenburg et al., 2007). Many high penetrant genes of DNA repair pathways (e.g., BRCA1 and BRCA2 etc.) are reported to be involved in inherited predisposition to breast cancer. The high pene- trant genes only explain 5% of breast cancer cases, thus, other low penetrant genes that have essential role in maintaining genomic in- tegrity may cause predisposition to breast cancer (Bau et al., 2007). Genomic variants of these genes significantly increase breast cancer risk and depict a major role of the DNA repair pathway in breast carcinogenesis (Kennedy et al., 2005). Several studies have investigated the role of single nucleotide polymorphisms (SNPs) in DNA repair genes in relation to breast cancer and have reported associations with breast cancer risk (Goode et al., 2002; Kuschel et al., 2002; ´a-Closas et al., 2006; Haiman et al., 2008). Based on these reports, it is suggested that SNPs in genes involved in DNA repair may influence DNA repair ca- pacity and, in turn, alter susceptibility to develop breast cancer. The XRCC4 gene is an important protein of non-homologous end-joining (NHEJ) repair pathway, that repairs DNA double-strand break (Li et al., 1995). The XRCC4 protein interacts directly with Ku70/Ku80 dimer, and its associated protein, ligase 4 (Lig4) (Mari et al., 2006). One study on gene-targeting mutation mouse model, found that XRCC4 gene in- activation led to late embryonic lethality, defective lymphogenesis and neurogenesis because of severe apoptotic death of newly generated neuronal cells (Gao et al., 1998). XRCC4 was also found to play a role in the age at diagnosis and risk of breast cancer in non-heritable cases https://doi.org/10.1016/j.gene.2018.02.040 Received 1 June 2017; Received in revised form 21 December 2017; Accepted 12 February 2018 ⁎ Corresponding author at: Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), ADIT Campus, New Vallabh Vidyanagar, Gujarat 388121, India. E-mail addresses: kinnarimistry@aribas.edu.in, kinnarinmistry@yahoo.com (K.N. Mistry). Abbreviations: ARMS, amplification-refractory mutation system; BER, base excision repair; CI, confidence interval; DDG, Gibbs free energy change; HWE, Hardy–Weinberg equilibrium; HMM, Hidden Markov Model; NCBI, National Centre for Biological Information; NHEJ, non-homologous end-joining; nsSNPs, non-synonymous single nucleotide polymorphisms; OR, odds ratio; PANTHER, Protein ANalysis THrough Evolutionary Relationships; PDB, Protein Data Bank; POLYPHEN, polymorphism phenotyping; PSIC, profile extraction from sequence alignments with position-specific counts; RI, reliability index; SIFT, sorting intolerant from tolerant; SNPs, single nucleotide polymorphisms; subPSEC, substitution position-specific evolutionary conservation Gene 655 (2018) 13–19 Available online 13 February 2018 0378-1119/ © 2018 Elsevier B.V. All rights reserved. T