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Capturing and Sequencing the Protein Coding Genome
Jay Shendure M.D., Ph.D., is Assistant Professor of Genome Sciences at the University of Washington.  

Next-generation sequencing technologies have reduced the cost of DNA sequencing by several orders of magnitude. While the routine resequencing of full human genomes continues to be prohibitively expensive for studies involving large numbers of individuals, the cost of resequencing the ~1% of the human genome that is protein-coding, may soon be on par with that of dense genotyping arrays. We are exploring several strategies for massively multiplex capture of discontiguous genomic subsequences, a prerequisite for efficient PCG resequencing. These include an approach based on oligonucleotide libraries derived from programmable microarrays, which then serve as Molecular Inversion Probes, while another approach involves using dense microarrays for capture-by-hybridization. By using HapMap samples and coupling both capture methods to high-throughput sequencing on the Illumina platform, we have observed high sensitivity and specificity for variant discovery at well-covered positions. Ongoing work is primarily directed at optimizing for capture uniformity and efficiency.

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