Genotyping was performed at the Broad Institute of Harvard and MIT. In the cases, out of the 1,199,187 variants analyzed by the Illumina 1M-Duo chip, 47 variants were discarded because they showed discordant clustering among different Illumina chips (private communication, Illumina Technical Support, August 11, 2009), 56,590 variants were excluded because more than 10% of genotypes were missing in African Americans and 58,524 were excluded for similar reasons in European Americans. In controls, out of 549,837 variants in African Americans, 7,298 variants were excluded because missing more than 10% of genotypes and out of 561,255 variants in European Americans 19,051 were excluded for the same reason. Almost all of the variants in the Illumina 550Kv3 chip are also included in the Illumina 1M-Duo chip, so there was not an additional loss of coverage when comparing results for the two platforms. Strand issues were not a concern, because C/G or A/T SNPs are not genotyped in the Illumina 550Kv3 platform — these polymorphisms can give rise to spurious case-control comparisons when other genotyping platforms are used, a frequent cause of problems if the data describing which strand is used to code the SNPs is incorrect or unavailable.
