All SNPs in dbSNP release 122 were considered for genotyping by Perlegen. Among these the following were excluded: SNPs for which no assay could be designed (primarily through location in repeat-rich regions; approximately 2.5 million); SNPs shown previously in samples from related populations15 to be most probably in perfect association (r2 = 1) with a Phase I SNP (approximately 122,000); all but one of SNPs shown previously15 to be most probably in perfect association (r2 = 1) with each other but not with a Phase I SNP (approximately 62,000); and SNPs shown previously15 to have MAF < 0.05 (approximately 119,000). In addition, a few SNPs were excluded for efficiency (for example, if an amplicon contained a single SNP). Approximately 30,000 SNPs that had been typed in Phase I were deliberately retyped in Phase II to allow detailed comparisons of data quality, and an additional 15,000 SNPs that showed discrepancies between multiple genotyping attempts in Phase I were re-typed in Phase II. A further 2,000 SNPs identified by the Mammalian Gene Collection were also typed.
