Detection of genomic variation by selection of a 9 Mb DNA region and high throughput sequencing

Sergey I. Nikolaev, Christian Iseli, Andrew J. Sharp, Daniel Robyr, Jacques Rougemont, Corinne Gehrig, Laurent Farinelli, Stylianos E. Antonarakis

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10 Scopus citations


Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb) and 7 (1.1 Mb) from an individual from the International HapMap Project (NA12872). We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage ≥ 4-fold, and 97.9% concordant in regions with coverage ≥ 15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants.

Original languageEnglish
Article numbere6659
JournalPLoS ONE
Issue number8
StatePublished - 17 Aug 2009
Externally publishedYes


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