PO-054 Common genetic variants at the breast cancer risk region 2Q35 map to putative IGFbp5 enhancers

Abstract

IntroductionGenome-wide association studies (GWAS) have identified over 100 independently-associated regions of the genome with germline variants that modulate risk of developing breast cancer. Most signals map to non-coding regions of the genome and are thought to act at the level of gene regulation. Whilst GWAS are instrumental in highlighting regions of interest, it is important to identify the causal variant(s) at each locus and the mechanisms by which they influence risk.Material and methodsWe investigated the 2q35 breast cancer risk locus using two complementary methods. The first method involved selecting potentially causal variants based primarily on breast relevant functional data (Capture Hi-C, ChIP-seq, DNase-seq, GRO-seq) The second method involved conventional fine-mapping of case-control samples, to generate a short list of potentially causal variants that cannot be excluded on statistical grounds alone followed by intersection of the same breast-relevant functional data.Results and discussionsThe two methods identify distinct subsets of putative causal SNPs mapping to ERα/FOXA1 enhancer-like elements targeting the IGFBP5 gene promoter, a gene known to play a role in breast development. We confirmed enhancer status by performing luciferase reporter assays containing each of the regions of interest; furthermore, by introducing minor SNP alleles we identified a subset of SNPs that modulate strength of enhancer activity. ChIP-seq in heterozygous cell lines also confirms an allelic preference in enhancer binding. We are now using CRISPR/Cas9-based systems to investigate the regions of interest through perturbation studies, and generating isogenic cell lines to further investigate SNP effects on transcription factor binding, chromosome conformation and gene expression.ConclusionThe 2q35 breast cancer risk locus consists of three independent risk-associated signals. Statistical and functional approaches to variant prioritisation are complementary, identifying largely overlapping but distinct sets of candidate causal variants in putative regulatory elements (PREs). Subsequent functional investigation suggests these genetic variants may modulate the strength of these PREs; however, further investigation in isogenic cell lines is required.