Allelotyping of pooled DNA with 250 K SNP microarrays

We could confirm that the polynomial based probe specific correction (PPC) was the most accurate method for allele frequency estimation. However, a simple k-correction, using the relative allele signal (RAS) of heterozygous individuals, performed only slightly worse and provided results for more SNPs. Using four replicates of the 250 K array and the k-correction using heterozygous RAS values, we obtained results for 104.141 SNPs. The correlation between estimated and real allele frequency was 0.983 and the average error was 0.046, which was comparable to the results obtained with the 10 K array. Furthermore, we could show how the estimation accuracy depended on the SNP type (average error for A/T SNPs: 0.043 and for G/C SNPs: 0.052).The combination of DNA pooling and analysis of single nucleotide polymorphisms (SNPs) on high density microarrays is a promising tool for whole genome association studies.To find new susceptibility loci for complex diseases on the human genome, a high number of case and control samples is required. An old approach with new perspective is the pooling of cases and controls. The larger the number of analyzed SNPs, the more striking are the advantages of a pooling study. With advanced microarray technology it is now possible to analyze SNPs throughout the whole genome. With the Human Mapping 500 K array set from Affymetrix and the BeadChips from Illumina, over 500,000 SNPs can be genotyped on two arrays. Different groups have tested the reliability of Affymetrix microarrays for pooling studies with either the 10 K array [1-6] or the 50 K array [7,8]. On these arrays, each SNP is interrogated by 40 probes (20 for the plus and 20 on the minus strand). On the 250 K arrays over 90% of the SNPs are represented by only 24 probes (some SNPs are only on the plus or the minus strand). This reduction of probes, as well as the reduction of the feature size from 18 μm (10 K), and 8 μm (50 K) to 5 μm (250 K) could have a negative influence on the outcome