Predicting allele frequencies in DNA pools using high density SNP genotyping data

Abstract

To evaluate the ability to use DNA pools with the Illumina Infinium genotyping platform, two sets of gradient pools were created using two pairs of highly inbred chicken lines. Replicate pools containing 0%, 10%, 20%, 40%, 60%, 80%, 90% and 100% of DNA from line A vs. B or line C vs. D were created, for a total of 28 pools. All pools were genotyped for 12,046 SNPs. Three frequency estimation methods proposed in the literature (standard, heterozygote-corrected and normalized) were compared with three alternate methods proposed herein based on mean square error (MSE), bias and variance of estimated vs. true allele frequencies and the fit of regression of estimated on true frequencies. The three new methods had average square root MSE of 4.6%, 4.6% and 4.7% compared to 5.2%, 5.5% and 11.2% for the three literature methods. Average absolute biases of the literature methods were 2.4%, 2.7% and 8.2% compared to 2.4% for all new methods. Standard deviations of estimates were also smaller for the new methods, at 3.1%, 3.2% and 3.2% compared to 3.5%, 4.0% and 5.0% for previously reported methods. In conclusion, intensity data from the Illumina Infinium Assay can be efficiently used to estimate allele frequencies in pools, in particular using any of the new methods proposed herein.