DNA was extracted from blood at each participating institution and Genizon BioSciences Inc. conducted genotyping with funding from Pfizer Inc. Genomic DNA samples from the MGH and WASH-U were genotyped using the Illumina Human1M BeadChip (N=1,057,265 SNPs) while the UCLA samples were genotyped using the Illumina Human 1M-Duo array (N=1,151,846 SNPs). Genotyping calls were generated after clustering all available data within platform at Genizon and then merged into a single file of 1,172,613 SNPs. To generate a data set of markers common to all sites, we removed SNPs that were either not included on both arrays (N=128,718 SNPs) or failed preliminary quality-control (QC) procedures conducted at Genizon (99% call rate for all samples and for all SNPs, gender check, Mendelian errors) on both the 1M and 1M-Duo arrays (N=9,500 SNPs), the 1M array only (N=39,753 SNPs) or the 1M-Duo array only (N=11,201 SNPs). Once the data from the multiple sites and different Illumina arrays were merged, there were 983,441 SNPs genotyped across the complete sample of 737 trios.
