Chapter 4 Microarray-Based Genome-Wide Association Studies Using Pooled DNA

Pooling genomic DNA samples within clinical classes of disease for use in whole-genome single nucleotide polymorphism (SNP) genotyping allows for rapid and inexpensive genome-wide association studies (GWAS). We describe here a general outline for combining hundreds of genomic DNA samples prior to genotyping on commercially available high-density SNP microarrays. The pool construction approach is universal, and independent of the SNP genotyping platform utilized, and therefore provides a quick, efficient, and low-cost alternative to interrogating thousands of individual samples on singular SNP microarrays. While the strategy for pooled DNA genotyping on SNP microarrays is straightforward, the success of such studies is critically dependent upon the accuracy of allelic frequency calculations, the ability to identify falsely positive results arising from assay variability, and the willingness to better resolve association signals through investigation of neighboring SNPs. Key words: Genome-wide association study, Single nucleotide polymorphism, DNA pooling, Equimolar concentration, Allelic frequency, GenePool While 99.9 % of the human genome sequence is identical in human beings, it is estimated that there are approximately ten million single nucleotide polymorphisms (SNPs) that, in combination, can distinguish among individuals (1–3). SNPs are nucleotide variants, for example, an adenosine to thymine (A/T) substitu-tion, that occur throughout the human genome. These variants can contribute directly to disease predisposition by modifying a gene’s function, or they can be used as genetic markers to detect nearby disease-causing mutations through association or family-based linkage studies. There are three general classes of SNPs: those with strong functional effects, which dramatically alter