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- Title
Microdroplet-based PCR enrichment for large-scale targeted sequencing.
- Authors
Tewhey, Ryan; Warner, Jason B.; Nakano, Masakazu; Libby, Brian; Medkova, Martina; David, Patricia H.; Kotsopoulos, Steve K.; Samuels, Michael L.; Hutchison, J. Brian; Larson, Jonathan W.; Topol, Eric J.; Weiner, Michael P.; Harismendy, Olivier; Olson, Jeff; Link, Darren R.; Frazer, Kelly A.
- Abstract
Targeted enrichment of specific loci of the human genome is a promising approach to enable sequencing-based studies of genetic variation in large populations. Here we describe an enrichment approach based on microdroplet PCR, which enables 1.5 million amplifications in parallel. We sequenced six samples enriched by microdroplet or traditional singleplex PCR using primers targeting 435 exons of 47 genes. Both methods generated similarly high-quality data: 84% of the uniquely mapping reads fell within the targeted sequences; coverage was uniform across ∼90% of targeted bases; sequence variants were called with >99% accuracy; and reproducibility between samples was high (r2 = 0.9). We scaled the microdroplet PCR to 3,976 amplicons totaling 1.49 Mb of sequence, sequenced the resulting sample with both Illumina GAII and Roche 454, and obtained data with equally high specificity and sensitivity. Our results demonstrate that microdroplet technology is well suited for processing DNA for massively parallel enrichment of specific subsets of the human genome for targeted sequencing.
- Subjects
GENE targeting; POLYMERASE chain reaction; NUCLEOTIDE sequence; GENE mapping; HUMAN genome; HUMAN genetic variation
- Publication
Nature Biotechnology, 2009, Vol 27, Issue 11, p1025
- ISSN
1087-0156
- Publication type
Article
- DOI
10.1038/nbt.1583