Subjects were drawn from two previous genome-wide association studies (GWAS), performed as part of the Cancer Genetic Markers of Susceptibility (CGEMS) project [51], [52]. Data on smoking behaviors were available on 2,060 men from the Prostate, Lung, Colon and Ovarian Trial (PLCO) (1,172 prostate cancer cases and 1,157 controls) and on 2,282 postmenopausal women (1,145 with breast cancer and 1,142 controls) from the Nurses' Health Study (NHS). All subjects were of self-reported European ancestry, which was consistent with genetic analyses of population structure [53]. Samples from the PLCO were genotyped using the Illumina HumanHap 300 k and HumanHap 240 k platforms [52]; those from the NHS were genotyped using the Illumina HumanHap 550 k platform [51]. Genotyping was performed at the same laboratory and similar genotyping quality control (QC) procedures were used in each study. Individual samples were removed if more than 10% of SNPs failed genotyping, and individual SNPs were removed if more than 10% of samples failed. The average call rate for both PLCO and NHS samples was 99.8%. Combined genome-wide analyses were restricted to directly-genotyped SNPs with
