Criteria for included SNPs were call rate >97% for autosomes, >98% for chromosome X in females or >99% in males; minor allele frequency >1%; Hardy-Weinberg P-value >10−6 in controls; <3 Mendelian errors detected in 30 MGS trios; <2 discordant duplicate genotypes in GenRED duplicates or <3 in 90 MGS specimens genotyped in both the GAIN and NonGAIN experiments; case-control call rate difference <2% for autosomes or <1% for X chromosome; and passing a 1df plate-effect test (no plate differing from all others with P<10−8, or <2 plates with P<10−4). Each SNP passed these criteria in both MGS and GenRED samples. After QC, 671,424 autosomal and 25,068 X chromosome SNPs were included.
