Follow-up set 1 (715 cases; 3,634 controls) was genotyped at UCLA on the HumanHap550 BeadChip and at deCODE Genetics on the HumanCNV370 BeadChip. Only the markers shown in Supplementary Table 3, however, were used in this study. Follow-up set 2 (3,330 cases; 6,892 controls) was genotyped at deCODE Genetics using Centaurus assays (Nanogen). Assay quality was evaluated by genotyping the CEU HapMap samples and comparing the results with the publicly released HapMap data. Assays with a greater than 1.5% mismatch rate were not used. Follow-up set 3 (287 cases; 3,987 controls) was typed in Finland using the Sequenom MassArray iPLEX genotyping system, following the manufacturer’s instructions (Sequenom Inc.). Briefly, the system involves multiplex PCR and mini-sequencing assays, followed by MALDI-TOF mass spectrometry analysis. Follow-up set 4 (667 cases; 1,042 controls) was typed at the Santiago de Compostela node of the Spanish National Genotyping Centre (http://www.cegen.org) using the Sequenom MassArray iPLEX genotyping system, following the manufacturer’s instructions (Sequenom Inc.). As a quality check, all clusters were manually inspected for accurate genotype assignment. In addition, 1,781 genotypes were successfully assayed twice, with no discordant results.
