July 7, 2019  |  

An integrated map of structural variation in 2,504 human genomes.

Authors: Sudmant, Peter H and Rausch, Tobias and Gardner, Eugene J and Handsaker, Robert E and Abyzov, Alexej and Huddleston, John and Zhang, Yan and Ye, Kai and Jun, Goo and Hsi-Yang Fritz, Markus and Konkel, Miriam K and Malhotra, Ankit and Stütz, Adrian M and Shi, Xinghua and Paolo Casale, Francesco and Chen, Jieming and Hormozdiari, Fereydoun and Dayama, Gargi and Chen, Ken and Malig, Maika and Chaisson, Mark J P and Walter, Klaudia and Meiers, Sascha and Kashin, Seva and Garrison, Erik and Auton, Adam and Lam, Hugo Y K and Jasmine Mu, Xinmeng and Alkan, Can and Antaki, Danny and Bae, Taejeong and Cerveira, Eliza and Chines, Peter and Chong, Zechen and Clarke, Laura and Dal, Elif and Ding, Li and Emery, Sarah and Fan, Xian and Gujral, Madhusudan and Kahveci, Fatma and Kidd, Jeffrey M and Kong, Yu and Lameijer, Eric-Wubbo and McCarthy, Shane and Flicek, Paul and Gibbs, Richard A and Marth, Gabor and Mason, Christopher E and Menelaou, Androniki and Muzny, Donna M and Nelson, Bradley J and Noor, Amina and Parrish, Nicholas F and Pendleton, Matthew and Quitadamo, Andrew and Raeder, Benjamin and Schadt, Eric E and Romanovitch, Mallory and Schlattl, Andreas and Sebra, Robert and Shabalin, Andrey A and Untergasser, Andreas and Walker, Jerilyn A and Wang, Min and Yu, Fuli and Zhang, Chengsheng and Zhang, Jing and Zheng-Bradley, Xiangqun and Zhou, Wanding and Zichner, Thomas and Sebat, Jonathan and Batzer, Mark A and McCarroll, Steven A and Mills, Ryan E and Gerstein, Mark B and Bashir, Ali and Stegle, Oliver and Devine, Scott E and Lee, Charles and Eichler, Evan E and Korbel, Jan O

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

Journal: Nature
DOI: 10.1038/nature15394
Year: 2015

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