We compared individual vs pooled allele frequency estimations for the ca. 500 SNPs that displayed minor allele frequencies >0.1 and provided clustered, nominally positive results in data from the NIDA pooled samples. The results from these SNPs displayed mean 0.66 Pearson correlation coefficients between data from pooled and individual genotyping. These correlations were more modest than those identified in validating studies for pooling that used larger ranges of expected allele frequencies. Thus, there was an average 0.19 range of expected values for these genotypes vs 0.9 range for the SNPs and pools used in initial studies that validated pooling with these Affymetrix 6.0 arrays) [21].
