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

Identifiers: SRA: SRP000001
BioProject: PRJNA33627
454MSC: HUMAN_SV
Study Type: 
Whole Genome Sequencing
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.
Center Project: Homo sapiens
External Link: /pubmed:17901297

Related SRA data

Experiments:
9 ( 2 samples )
Runs:
83 (9.7Gbp; 22.3Gb)