Replication genotyping was performed using the TaqMan genotyping platform in 8 participating genotyping laboratories (Table 4). The robustness of the Taqman assays (primers and probes are available upon request) were confirmed at IARC by re-genotyping the CEPH HapMap (CEU) trios and confirming concordance with HapMap genotypes. Any discordance between Hapmap and Taqman generated genotypes was resolved by direct DNA sequencing. All Taqman assays were found to be performing robustly. IARC supplied Taqman assays and a standardized Taqman genotyping protocol to each of the 8 participating genotyping laboratories. A common series of 90 standard DNAs were genotyped at each laboratory to ensure the quality and comparability of the genotyping results across the different studies. Concordance with the consensus genotype and the results produced at the eight genotyping laboratories for the standardized DNAs was 99.75%, and no individual centre had a overall concordance of less than 99.5%. If the assay produced 2 or more discordant genotypes relative to the consensus, the study genotypes for this genetic variant were not included in the statistical analysis. Assays that had a per-centre success rate of <90% or for which genotype distributions deviated from HWE (p<0.001) were also excluded (Table S5).
