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Feb 15, 2009 (Vol. 29, No. 4)

Honing In on Targeted Resequencing

Researchers Revisit the Human Genome to Identify Disease-Associated Variants

  • Protein-Coding Genome

    While the cost of resequencing a complete human genome has dropped from millions of dollars to about $25,000-100,000, it is still a very expensive project, says Jay Shendure, assistant professor, genome sciences, University of Washington. “We are far away from the $1,000 genome, but we are making strides.”

    Dr. Shendure’s group is examining how to more efficiently isolate and study complex genome subsets. “We are exploring several experimental strategies for massive  multiplex capture of discontiguous genomic subsequences. This is a prerequisite for efficient sequencing of the protein coding genome (PCG), which amounts to about 1% of the entire human genome.”

    The PCG is an important genomic subset that would allow more economical screening of many individuals instead of examining the whole genome of fewer individuals. “It all depends on where you think the relevant and interpretable variation will be. Protein-coding variation is more amenable to interpretation and follow-up than regulatory variation.  For every complete human genome that you sequence, you could instead characterize 10–100 times as many PCGs.”

    Dr. Shendure is working to optimize a next-generation sequencing strategy that uses microarrays. “Microarrays are useful for direct capture-by-hybridization of sequences of interest, and we are pursuing this. We have also shown that a complex mixture of molecular inversion probes obtained by parallel synthesis on and release from the surface of a programmable microarray can capture approximately 50,000 exons in a single reaction. We’re currently evaluating which of several potential methods for PCG capture will be the most robust and scalable.”

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