Genotyping was performed by the Center for Inherited Disease Research (CIDR). DNA sources included blood (n=1453) and lymphoblastoid cell lines (LCL, n=492). Genotyping was performed using the Illumina Infinium II assay protocol (Gunderson et al., 2006) with hybridization to Illumina HumanHap1M BeadChips (Illumina, San Diego, CA, USA), which contain 1,199,187 markers with a mean spacing of 2.4 kb. Allele cluster definitions for each SNP were determined using Illumina BeadStudio Genotyping Module version 3.1.14 and the combined intensity data from 96% of study samples. The resulting cluster definition file was used on all study samples to determine genotype calls and quality scores. Genotype calls were made when a genotype yielded a quality score (Gencall value) of 0.15 or higher. The final raw dataset released by CIDR to the investigators and to dbGaP contained 1,041,465 SNPs for 1,945 unique DNA samples from case and control subjects. Twenty seven samples were removed due to poor sample quality before release of the dataset on dbGaP (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap; Accession number: phs000125.v1.p1). Blind duplicate reproducibility was 99.97%.
