using these platforms and Affymetrix SNP Array 6.0 based on 1,478,383 comparisons (mean, 99.1%; median, 99.8%). Samples with genotyping call rates less than 95% were excluded, and the remaining samples were recalled by using Birdseed v2. The gender of all study samples was confirmed to be female. The identity-by-descent analysis based on identity-by-state was performed to detect first degree cryptic relationships using the PLINK 1.04 25 (http://pngu.mgh.harvard.edu/purcell/plink/). A final data set included 3,027 individuals and 607,728 markers in the Affymetrix SNP Array 6.0 and 330,885 in the Affymetrix 500K Array Set that met the following criteria: (1) genotype call rate ≥ 95%; (2) MAF ≥ 5%; and (3) genotyping concordance rate in QC samples ≥ 95%. Also excluded from the analyses were 21,223 SNPs that are on Affymetrix 500K Array Set but not on the SNP Array 6.0.
