Both the genome-wide scans used in this study analyzed approximately 550,000 SNPs on the Illumina platform. The prostate cancer study genotyped cases and matched controls collected from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial using the HumanHap300 (Illumina, San Diego, CA) and HumanHap240 chips (Illumina, San Diego, CA) [1]. The breast cancer scan used the HumanHap550 chip (Illumina, San Diego, CA), which is equivalent to the HumanHap300 and HumanHap240 chips combined, to genotype cases and their matched controls collected from the Nurses' Health Study (NHS) cohort [2]. In both studies, participants were restricted to individuals who were of self-described European descent. Quality control and quality assessment removed subjects with low completion rates (<90%), subjects with evidence of an intercontinental admixture (European admixture coefficient less than 90%, estimated by STRUCTURE [19]), and removal of one of each pair of first-degree relatives (identified using PREST [22]). No second degree relatives were detected. For this study, the test set for the PLCO prostate cancer study consisted of 1,171 prostate cancer cases and 1,094 controls while the test set for the
