Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer

The somatic mutations in a cancer genome are the aggregate outcome of one or more mutational processes operative through the life of the cancer patient(1-3). Each mutational process leaves a characteristic mutational signature determined by the mechanisms of DNA damage and repair that constitute it. A role was recently proposed for the APOBEC family of cytidine deaminases in generating particular genome-wide mutational signatures(1,4) and a signature of localized hypermutation called kataegis(1,4). A germline copy number polymorphism involving APOBEC3A and APOBEC3B, which effectively deletes APOBEC3B(5), has been associated with a modest increased risk of breast cancer(6-8). Here, we show that breast cancers in carriers of the deletion show more mutations of the putative APOBEC-dependent genome-wide signatures than cancers in non-carriers. The results suggest that the APOBEC3A/3B germline deletion allele confers cancer susceptibility through increased activity of APOBEC-dependent mutational processes, although the mechanism by which this occurs remains unknown.