Accuracy of allele frequency estimates in pool DNA analyzed by high-density Illumina Human 610-Quad microarray

Abstract

Purpose: DNA pooling method has been previously proven successful for allele frequency estimation using earlier versions of Illumina Beadchip and Affymetrix GeneChip microarrays. The aim of this study was to evaluate the accuracy of the DNA pooling using the High Density Illumina Infinium microarray system.Patients & methods: The accuracy of three different methods of allele frequency estimation on the High Definition Infinium II Beadchip (Human 610-Quad) was tested using the DNA samples obtained from saliva collected from seven Caucasian subjects who had been individually genotyped. Our first approach was to calculate estimated allelic frequency (expressed as B allele frequency) from pooled DNA sample based on the correlation coefficient obtained for individual SNPs, and to correlate it with the true (real) allele frequency computed using individually genotyped samples. The second approach was to estimate SNP frequency in the pooled DNA sample as calculated automatically by the proprietary Beadstudio software, which is based on the internal calibration and normalization procedures. The third approach was to study the pool allele frequency calculated using the estimation of correlation coefficient from microarray SNP sub-pools.Results and conclusions: All analyzed methods of allelic frequency estimates from pooled DNA produced similar results in respect to the calculated correlation coefficient (R) (R ranging from 0.947 to 0.958 with R>0.99 for correlation between each three of them). All three methods of calculations seem to be sufficient and equally effective for calculation of individual allelic frequency for the given SNPs from the pooled DNA.