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| Status |
Public on Sep 28, 2007 |
| Title |
8-chip high-resolution aCGH experiment NA15510 vs. NA18505 |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 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 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 deduced with a novel pooling strategy and computational analysis. Array-CGH was used for validation.
Keywords: array CGH
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| Overall design |
2 samples were analyzed with 8 different Nimblegen chips (385k); thus ~30M probes were used to interrogate copy number variants in NA15510 (using NA18505 as control) at high resolution.
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| Contributor(s) |
Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero N, Du L, Taillon B, Tanzer A, Saunders E, Chi J, Yang F, Carter N, Hurles M, Weissman S, Harkins TT, Gerstein MB, Egholm M, Snyder M, Chen Z |
| Citation(s) |
17901297 |
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| Submission date |
Sep 10, 2007 |
| Last update date |
Mar 17, 2012 |
| Contact name |
Jan Oliver Korbel |
| Phone |
+1 203 432 5405
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| Fax |
+1 203 432 5175
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| URL |
http://bioinfo.mbb.yale.edu/array/
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| Organization name |
Yale University
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| Street address |
266 Whitney Avenue
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
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| Platforms (8)
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| GPL5814 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (1 of 8) |
| GPL5815 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (2 of 8) |
| GPL5816 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (3 of 8) |
| GPL5817 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (4 of 8) |
| GPL5818 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (5 of 8) |
| GPL5819 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (6 of 8) |
| GPL5820 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (7 of 8) |
| GPL5821 |
NimbleGen Homo sapiens HG18 Whole Genome CGH Tiling Set (8 of 8) |
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| Samples (8)
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| GSM227608 |
CGH WG-set_1of8 NA18505 vs. NA15510 |
| GSM228515 |
CGH WG-set_2of8 NA18505 vs. NA15510 |
| GSM228516 |
CGH WG-set_3of8 NA18505 vs. NA15510 |
| GSM228517 |
CGH WG-set_4of8 NA18505 vs. NA15510 |
| GSM228519 |
CGH WG-set_5of8 NA18505 vs. NA15510 |
| GSM228521 |
CGH WG-set_6of8 NA18505 vs. NA15510 |
| GSM228522 |
CGH WG-set_7of8 NA18505 vs. NA15510 |
| GSM228524 |
CGH WG-set_8of8 NA18505 vs. NA15510 |
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| Relations |
| BioProject |
PRJNA102481 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9002_RAW.tar |
287.1 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
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