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SRX000002: 454 sequencing of Human HapMap individual NA15510 genomic paired-end library
12 LS454 (454 GS FLX) runs: 5.1M spots, 1.4G bases, 3.2Gb downloads

Design: none provided
Submitted by: 454 Life Sciences (454MSC)
Study: Paired-end mapping reveals extensive structural variation in the human genome
show Abstracthide 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.
Sample: HapMap sample from Homo sapiens
SAMN00000376 • SRS000605 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: SID2438
Instrument: 454 GS FLX
Strategy: WGS
Source: GENOMIC
Selection: RANDOM
Layout: PAIRED
Spot descriptor:
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Runs: 12 runs, 5.1M spots, 1.4G bases, 3.2Gb
Run# of Spots# of BasesSizePublished
SRR000004307,73278.1M194.4Mb2008-04-04
SRR000014527,848144.4M336.9Mb2008-04-04
SRR000017515,632141.2M331.6Mb2008-04-04
SRR000023468,650128.3M296.6Mb2008-04-04
SRR000029387,459105.4M247.5Mb2008-04-04
SRR000030456,302124.9M274.5Mb2008-04-04
SRR000036505,460138.3M322.8Mb2008-04-04
SRR000037283,03676.4M181.4Mb2008-04-04
SRR000040475,022130.3M306.5Mb2008-04-04
SRR000051471,503128.4M299.3Mb2008-04-04
SRR000053257,25370.4M163.1Mb2008-04-04
SRR000055424,980115.8M272.1Mb2008-04-04

ID:
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