Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci

Abstract

Breast Cancer (BCa) genome-wide association studies revealed allelic frequency differences between cases and controls at index single nucleotide polymorphisms (SNPs). To date, 71 loci have thus been identified and replicated. More than 320,000 SNPs at these loci define BCa risk due to linkage disequilibrium (LD). We propose that BCa risk resides in a subgroup of SNPs that functionally affects breast biology. Such a shortlist will aid in framing hypotheses to prioritize a manageable number of likely disease-causing SNPs. We extracted all the SNPs, residing in 1 Mb windows around breast cancer risk index SNP from the 1000 genomes project to find correlated SNPs. We used FunciSNP, an R/Bioconductor package developed in-house, to identify potentially functional SNPs at 71 risk loci by coinciding them with chromatin biofeatures. We identified 1,005 SNPs in LD with the index SNPs (r2≥0.5) in three categories; 21 in exons of 18 genes, 76 in transcription start site (TSS) regions of 25 genes, and 921 in enhancers. Thirteen SNPs were found in more than one category. We found two correlated and predicted non-benign coding variants (rs8100241 in exon 2 and rs8108174 in exon 3) of the gene, ANKLE1. Most putative functional LD SNPs, however, were found in either epigenetically defined enhancers or in gene TSS regions. Fifty-five percent of these non-coding SNPs are likely functional, since they affect response element (RE) sequences of transcription factors. Functionality of these SNPs was assessed by expression quantitative trait loci (eQTL) analysis and allele-specific enhancer assays. Unbiased analyses of SNPs at BCa risk loci revealed new and overlooked mechanisms that may affect risk of the disease, thereby providing a valuable resource for follow-up studies.

Investigation of gene‐environment interactions between 47 newly identified breast cancer susceptibility loci and environmental risk factors

“…The potentially functional implications of rs6828523 or SNPs highly correlated with rs6828523 (r 2 >0.6) are unclear as they are not located within any strong regulatory elements (Supplementary Figure 3). Also, a more comprehensive investigation of the functional effects of the 41 SNPs associated with overall breast cancer risk did not identify a SNP in LD with rs6828523 coinciding with a regulatory genomic feature 30 . ADAM29 encodes a disintegrin-metalloproteinase.…”

“…Furthermore, ELL has been found to be essential for the transcription of rapidly induced genes, and therefore plays a key role in quick responses to environmental changes 34 . Rhie et al identified another SNP (rs2303696) in LD with rs4808801 (r 2 = 0.79) located in the promoter region of ISYNA1, and likely to affect ISYNA1 expression 30 . ISYNA1 encodes an inositol-3-phosphate synthase enzyme that catalyses the synthesis of inositol 1-phosphate from glucose 6-phosphate.…”

“…ISYNA1 encodes an inositol-3-phosphate synthase enzyme that catalyses the synthesis of inositol 1-phosphate from glucose 6-phosphate. ISYNA1 expression has been found to be reduced in breast cancer 30 . Inositol containing compounds are involved in many biological processes and act as essential second messenger molecules in signalling pathways 35 , as components of cellular membranes 35 and regulators of chromatin remodelling 36, 37 .…”

“…Two SNPs in LD with rs11242675 are located in enhancer regions 30 . FOXQ1 is a transcription factor, which has been found to be involved in the epithelial-mesenchymal transition of tumour cells, a process initiating metastasis 39 .…”

SNP variants at the MAP3K1/SETD9 locus 5q11.2 associate with somatic PIK3CA variants in breast cancers

“…Twenty-one SNVs were selected (Supplementary Table S1): 11 from O'Brien et al, 9 rs889312, an expression quantitative trait locus (eQTL) SNV, 10,11 and three further SNVs in high linkage disequilibrium (LD) with the former all located at 5q11.2 (Supplementary Table S2), as well as seven further SNVs were selected from Rhie et al 12 We preferred SNVs associated with oestrogen receptor α-positive (ER+) BC risk (often higher than for all BC) and close to coding sequences, to maximise the use of genotyped data without imputations of allelic variant status.…”