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PLoS One. 2011 Mar 30;6(3):e18353. doi: 10.1371/journal.pone.0018353.

Efficient and cost effective population resequencing by pooling and in-solution hybridization.

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  • 1Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, California, United States of America. vbansal@scripps.edu

Abstract

High-throughput sequencing of targeted genomic loci in large populations is an effective approach for evaluating the contribution of rare variants to disease risk. We evaluated the feasibility of using in-solution hybridization-based target capture on pooled DNA samples to enable cost-efficient population sequencing studies. For this, we performed pooled sequencing of 100 HapMap samples across ∼ 600 kb of DNA sequence using the Illumina GAIIx. Using our accurate variant calling method for pooled sequence data, we were able to not only identify single nucleotide variants with a low false discovery rate (<1%) but also accurately detect short insertion/deletion variants. In addition, with sufficient coverage per individual in each pool (30-fold) we detected 97.2% of the total variants and 93.6% of variants below 5% in frequency. Finally, allele frequencies for single nucleotide variants (SNVs) estimated from the pooled data and the HapMap genotype data were tightly correlated (correlation coefficient >  =  0.995).

PMID:
21479135
[PubMed - indexed for MEDLINE]
PMCID:
PMC3068187
Free PMC Article

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