Whole-genome genotyping of haplotype tag single nucleotide polymorphisms.

The International HapMap Consortium recently completed genotyping over 3.8 million single nucleotide polymorphisms (SNPs) in three major populations, and the results of studying patterns of linkage disequilibrium indicate that characterization of 300,000–500,000 tag SNPs is sufficient to provide good genomic coverage for linkage-disequilibrium-based association studies in many populations. These whole-genome association studies will be used to dissect the genetics of complex diseases and pharmacogenomic drug responses. As such, the development of a cost-effective genotyping platform that can assay hundred of thousands of SNPs across thousands of samples is essential. In this review, we describe the development of a whole-genome genotyping (WGG) assay that enables unconstrained SNP selection and effectively unlimited multiplexing from a single sample preparation. The development of WGG in concert with high-density BeadChips™ has enabled the creation of three different high-density SNP genotyping BeadChips: the Sentrix™ Human-1 Genotyping BeadChip containing over 109,000 exon-centric SNPs; the HumanHap300 BeadChip containing over 317,000 tag SNPs, and the HumanHap550 Beadchip containing over 550,000 tag SNPs. The goal of pharmacogenomics is to use individual’s genetic information to improve patient diagnosis, prognosis, and therapeutic intervention [1]. Genetic differences between individuals within a population underlie an individual’s predisposition to maintain health, develop disease, and respond efficaciously or adversely to drug therapy [2–4]. Human genetic variation is characterized, in part, by the presence of over 10 million relatively common, single nucleotide polymorphisms (SNPs) in the human genome. The linkage disequilibrium (LD) patterns observed in human population reveal a blocklike structure; SNPs within a high LD region (termed haploype block) tend to be transmitted together from generation to generation [5,6]. As such, a set of tag SNPs that serve as proxies for other SNPs can be chosen based on levels of correlation between their alleles [7,8]. The use of tag SNPs greatly reduces the genotyping burden in association studies, since a fewer number of tag SNPs need to be genotyped while maintaining the same information and power as if one had genotyped a much larger number of random SNPs [9]. The objective of the HapMap project was to delineate the haplotype block structure of the human genome and provide data for the identification of tag SNPs across multiple populations with ancestry from parts of Africa, Asia and Europe. The HapMap project completed both Phase I and II in late 2005 [10]; the resulting haplotype analysis of the data indicates that approximately 300,000 tag SNPs will provide good coverage for the European (CEU, Utah residents with ancestry from Northern and Western Europe) and Asian populations (CHB, Han Chinese in Beijing, China and JPT, Japanese in Tokyo, Japan), and a set of over 500,000 tag SNPs will provide improved coverage for European and Asian populations and good coverage for an African population (YRI, Yoruba in Ibadan, Nigeria) [10]. Infinium whole-genome genotyping platform We developed a whole-genome genotyping technology, known as the Infinium™ assay (Figure 1A), to enable genotyping of hundreds of thousand of SNPs on a single BeadChip™ substrate (slide). The whole-genome genotyping assay was developed to mirror the scalability of an array-based gene expression assay in which a simple singletube sample preparation allows readout of an entire transcriptome [11]. To make the assay inherently scalable, the Infinium assay employs a direct hybridization of a single-tube whole-genome amplified (WGA) DNA sample to an array of oligonucleotide capture probes (50-mers). The WGA step amplifies the input genomic DNA (gDNA) present at a few hundred nanograms by over 1000×, leading to hundreds of micrograms of WGA product. This high concentration of target drives the hybridization capture of the target loci to the probes on the array. Following capture of