Mapping copy number variation by population-scale genome sequencing

Mills, Ryan E., Walter, Klaudia, Stewart, Chip, Handsaker, Robert E., Chen, Ken, Alkan, Can, Abyzov, Alexej, Yoon, Seungtai Chris, Ye, Kai, Cheetham, R. Keira, Chinwalla, Asif, Conrad, Donald F., Fu, Yutao, Grubert, Fabian, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Iakoucheva, Lilia M., Iqbal, Zamin, Kang, Shuli, Kidd, Jeffrey M., Konkel, Miriam K., Korn, Joshua, Khurana, Ekta, Kural, Deniz, Lam, Hugo Y. K., Leng, Jing, Li, Ruiqiang, Li, Yingrui, Lin, Chang-Yun, Luo, Ruibang, Mu, Xinmeng Jasmine, Nemesh, James, Peckham, Heather E., Rausch, Tobias, Scally, Aylwyn, Shi, Xinghua, Stromberg, Michael P., Stuetz, Adrian M., Urban, Alexander Eckehart, Walker, Jerilyn A., Wu, Jiantao, Zhang, Yujun, Zhang, Zhengdong D., Batzer, Mark A., Ding, Li, Marth, Gabor T., McVean, Gil, Sebat, Jonathan, Snyder, Michael, Wang, Jun, Ye, Kenny, Eichler, Evan E., Gerstein, Mark B., Hurles, Matthew E., Lee, Charles, McCarroll, Steven A. and Korbel, Jan O. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470 7332: 59-65. doi:10.1038/nature09708

Author Mills, Ryan E.
Walter, Klaudia
Stewart, Chip
Handsaker, Robert E.
Chen, Ken
Alkan, Can
Abyzov, Alexej
Yoon, Seungtai Chris
Ye, Kai
Cheetham, R. Keira
Chinwalla, Asif
Conrad, Donald F.
Fu, Yutao
Grubert, Fabian
Hajirasouliha, Iman
Hormozdiari, Fereydoun
Iakoucheva, Lilia M.
Iqbal, Zamin
Kang, Shuli
Kidd, Jeffrey M.
Konkel, Miriam K.
Korn, Joshua
Khurana, Ekta
Kural, Deniz
Lam, Hugo Y. K.
Leng, Jing
Li, Ruiqiang
Li, Yingrui
Lin, Chang-Yun
Luo, Ruibang
Mu, Xinmeng Jasmine
Nemesh, James
Peckham, Heather E.
Rausch, Tobias
Scally, Aylwyn
Shi, Xinghua
Stromberg, Michael P.
Stuetz, Adrian M.
Urban, Alexander Eckehart
Walker, Jerilyn A.
Wu, Jiantao
Zhang, Yujun
Zhang, Zhengdong D.
Batzer, Mark A.
Ding, Li
Marth, Gabor T.
McVean, Gil
Sebat, Jonathan
Snyder, Michael
Wang, Jun
Ye, Kenny
Eichler, Evan E.
Gerstein, Mark B.
Hurles, Matthew E.
Lee, Charles
McCarroll, Steven A.
Korbel, Jan O.
Title Mapping copy number variation by population-scale genome sequencing
Journal name Nature   Check publisher's open access policy
ISSN 0028-0836
Publication date 2011-02-03
Year available 2011
Sub-type Article (original research)
DOI 10.1038/nature09708
Open Access Status Not yet assessed
Volume 470
Issue 7332
Start page 59
End page 65
Total pages 7
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Language eng
Abstract Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
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