Targeted Resequencing of the Coding Sequence of 38 Genes Near Breast Cancer GWAS Loci in a Large Case–Control Study

Background: Genes regulated by breast cancer (BC) risk alleles identified through genome-wide association studies (GWAS) may harbour rare coding risk alleles. Methods: We sequenced the coding regions for 38 genes within 500kb of 38 lead GWAS SNPs in 13,538 breast cancer cases and 5,518 controls. Results: Truncating variants in these genes were rare, and were not associated with BC risk. Burden testing of rare missense variants highlighted five genes with some suggestion of an association with BC, though none met the multiple testing threshold: MKL1, FTO, NEK10, MDM4, and COX11. Six common alleles in COX11, MAP3K1 (two), and NEK10 (three) were associated at the P<0.0001 significance level, but these likely reflect linkage disequilibrium with causal regulatory variants. Conclusions: There was no evidence that rare coding variants in these genes confer substantial breast cancer risks. However, more modest effect sizes could not be ruled out. Impact: We tested the hypothesis that rare variants in 38 genes near breast cancer GWAS loci may mediate risk. These variants do not appear to play a major role breast cancer heritability.