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This chapter outlines methods for studying the genetic basis of psychiatric disorders. The two types of methods, single nucleotide polymorphism (SNP) genotyping and sequencing, are focused on characterizing two different types of variants predisposing to disease: common and rare. The chapter provides a technical overview of two technologies that have been used in the majority of linkage studies and population-based genome-wide association studies (GWAS): Illumina BeadArray Mapping arrays and Affymertrix Gene-Chip Arrays. While there are many potential applications of these technologies, the chapter focuses on those involving sequencing DNA for the purpose of identifying the genetic basis of disease, specifically dividing this section into targeted methods and genome-wide approaches. The chapter provides an overview of features for all three commercially available platforms (SOLiD, GA and 454). Analysis of next-generation sequencing data falls into three categories: alignment/assembly; quality control; and variant calling.
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