Multiplex amplification of large sets of human exons

Abstract

A new generation of technologies is poised to reduce DNA sequencing costs by several orders of magnitude. But our ability to fully leverage the power of these technologies is crippled by the absence of suitable 'front-end' methods for isolating complex subsets of a mammalian genome at a scale that matches the throughput at which these platforms will routinely operate. We show that targeting oligonucleotides released from programmable microarrays can be used to capture and amplify ~10,000 human exons in a single multiplex reaction. Additionally, we show integration of this protocol with ultra-high-throughput sequencing for targeted variation discovery. Although the multiplex capture reaction is highly specific, we found that nonuniform capture is a key issue that will need to be resolved by additional optimization. We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing. NOTE: In the version of this article initially published online,the affiliation for Jay Shendure was listed as Department of Computer Science, Virginia Commonwealth University,601 West Main Street,Richmond,Virginia 23284,USA. The correct affiliation should be Department of Genome Sciences,University of Washington,1705 NE Pacific St.,Seattle,Washington 98195,USA. The error has been corrected for all versions of the article.