SNPs were assayed using Sequenom technology for the AGP samples at three centers, namely Gulbenkian, Mt. Sinai, and Oxford: DNA from 1,629 families representing numerous recruiting sites was genotyped for 54 SNPs. SNPs with >3% missing data, namely rs4690464, rs10513025, and rs17088296, were excluded from analysis. The next step in our quality control process was to remove families with ≥4 Mendelian errors, out of 51 remaining loci, under the assumption that this indicated pedigree errors. Data from 110 families were removed due to Mendelian errors. Thereafter, SNPs were removed if they showed excessive Mendelian errors (>16) in the remaining families. Using this criterion, two more SNPs, rs155437 and rs1925058, were removed from analysis. It was apparent that DNA quality varied by study site and could be responsible for concomitant genotype quality differences. Therefore, we also evaluated rate of missing genotypes per locus and study site. Our analyses showed that DNA from a few population samples showed excess missingness for two SNPs, rs4742408 and rs7869239, relative to the remaining population samples. Specifically three population samples showed more than 7% missing genotypes
