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Title

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

Authors
Nikolaev, S. I.
Iseli, Christian
Sharp, A. J.
Published in PLOS ONE. 2009, vol. 4, no. 8, p. e6659
Abstract 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 > or = 4-fold, and 97.9% concordant in regions with coverage > or = 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.
Keywords Chromosome MappingChromosomes, Human, Pair 21DNA/*genetics*Genetic Variation*Genome, HumanHumansPolymorphism, Single Nucleotide
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PMID: 19684856
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NIKOLAEV, S. I. et al. Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing. In: PLOS ONE, 2009, vol. 4, n° 8, p. e6659. https://archive-ouverte.unige.ch/unige:9231

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Deposited on : 2010-07-12

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