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

Academic Article
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Overview

authors

  • Bansal, V.
  • Tewhey, R.
  • LeProust, E. M.
  • Schork, Nicholas

publication date

  • March 2011

journal

  • PLoS One  Journal

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).

subject areas

  • Cost-Benefit Analysis
  • Gene Frequency
  • Genetics, Population
  • Genome, Human
  • Humans
  • INDEL Mutation
  • Nucleic Acid Hybridization
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA
  • Solutions
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Identity

PubMed Central ID

  • PMC3068187

International Standard Serial Number (ISSN)

  • 1932-6203

Digital Object Identifier (DOI)

  • 10.1371/journal.pone.0018353

PubMed ID

  • 21479135
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Additional Document Info

start page

  • e18353

volume

  • 6

issue

  • 3

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