forHigh - Throughput Genotyping

The genetics of complex diseases has been given a tremendous boost in recent years by the introduction of high-throughput laboratory methods that allow us to approach larger questions in larger populations and to cover the genome more comprehensively. The ability to determine genotypes of many individuals accurately and efficiently has allowed genetic studies that cover more of the variation within individual genes, instead of focusing only on one or a few coding variants, and to do so in study samples of reasonable power. Chip-based genotyping assays, combined with knowledge of the patterns of coinheritance of markers (linkage disequilibrium, LD) developed through the HapMap Project (http://www. hapmap.org), have stimulated genome-wide association studies (GWAS) of complex diseases. These are being encouraged and supported by the National Institutes of Health (NIH) and other groups, notably The Wellcome Trust. Recent successes of GWAS in identifying specific genes that affect risk for common diseases are dramatic illustrations of how improved technology can lead to scientific breakthroughs. Rapid developments in high-throughput sequencing may enable new kinds of studies. A key issue in high-throughput genotyping is to choose the appropriate technology for your goals and for the stage of your experiment, being cognizant of your sample numbers and resources. This chapter introduces some of the commonly used methods of high-throughput single-nucleotide polymorphism (SNP) genotyping for different stages of genetic studies and briefly reviews some of the high-throughput sequencing methods just coming into use. We will also note some recent developments in “next-generation” sequencing that will enable other kinds of studies. We cannot be comprehensive, and technology in this area is rapidly changing, so our comments should be taken as a starting point for further investigation. For simplicity, we will discuss three main types of studies: candidate genes, linkage studies and their follow-up, and GWAS and their follow-up. There are choices of genotyping technologies suited to each of these types of studies (Fig. 16.1). Throughput, cost per SNP genotype, and costs per sample can be very different for different technologies. Some technologies, which we call “serial,” allow testing of small to modest numbers of SNPs on many subjects in each reaction and are easy to customize. Others, called “parallel” methods, test up to a million SNPs on each subject at one time in fixed panels. The cost per SNP for a serial method is much larger than for a parallel method, but the cost per subject is much less. Howard J. Edenberg1 and Yunlong Liu2