For several years, the genome-wide association study (GWAS) has served as the flagship discovery tool for genetic research, especially in the arena of common diseases. The wide availability and low cost of high-density SNP arrays made it possible to genotype 500,000 or so informative SNPs in thousands of samples. These studies spurred development of tools and pipelines for managing large-scale GWAS, and thus far they’ve revealed hundreds of new genetic associations.
As we all know, the cost of DNA sequencing has plummeted. Now it’s possible to do targeted, exome, or even whole-genome sequencing in cohorts large enough to power GWAS analyses. While we can leverage many of the same tools and approaches developed for SNP array-based GWAS, the sequencing data comes with some very important differences.
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