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Science. 2007 Oct 19;318(5849):420-6. Epub 2007 Sep 27.

Paired-end mapping reveals extensive structural variation in the human genome.

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  • 1Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.

Abstract

Structural variation of the genome involves kilobase- to megabase-sized deletions, duplications, insertions, inversions, and complex combinations of rearrangements. We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome-sequencing method to identify structural variants (SVs) approximately 3 kilobases (kb) or larger that combines the rescue and capture of paired ends of 3-kb fragments, massive 454 sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and in a putatively European individual and identified shared and divergent SVs relative to the reference genome. Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were determined with a novel pooling strategy and computational analysis. Our analysis provided insights into the mechanisms of SV formation in humans.

PMID:
17901297
[PubMed - indexed for MEDLINE]
PMCID:
PMC2674581
Free PMC Article
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