Pooled versus individual genotyping in a breast cancer genome-wide association study

We examine the measurement properties of pooled DNA odds ratio estimates for 7,357 single nucleotide polymorphisms (SNPs) genotyped in a genome-wide association study of postmenopausal breast cancer. This study involved DNA pools formed from 125 cases or 125 matched controls. Individual genotyping for these SNPs subsequently came available for a substantial majority of women included in seven pool pairs, providing the opportunity for a comparison of pooled DNA and individual odds ratio estimates and their variances. We find that the "per minor allele" odds ratio estimates from the pooled DNA comparisons agree fairly well with those from individual genotyping. Furthermore, the log-odds ratio variance estimates support a pooled DNA measurement model that we previously described, although with somewhat greater extra-binomial variation than was hypothesized in project design. Implications for the role of pooled DNA comparisons in the future genetic epidemiology research agenda are discussed.