| Literature DB >> 33632895 |
Peter Ebert1, Peter A Audano2, Qihui Zhu3, Bernardo Rodriguez-Martin4, Charles Lee5,6,7, Jan O Korbel8,9, Tobias Marschall10, Evan E Eichler11,12, David Porubsky2, Marc Jan Bonder4,13, Arvis Sulovari2, Jana Ebler1, Weichen Zhou14, Rebecca Serra Mari1, Feyza Yilmaz3, Xuefang Zhao15,16, PingHsun Hsieh2, Joyce Lee17, Sushant Kumar18, Jiadong Lin19, Tobias Rausch4, Yu Chen20, Jingwen Ren21, Martin Santamarina22,23, Wolfram Höps4, Hufsah Ashraf1, Nelson T Chuang24, Xiaofei Yang25, Katherine M Munson2, Alexandra P Lewis2, Susan Fairley9, Luke J Tallon24, Wayne E Clarke26, Anna O Basile26, Marta Byrska-Bishop26, André Corvelo26, Uday S Evani26, Tsung-Yu Lu21, Mark J P Chaisson21, Junjie Chen27, Chong Li27, Harrison Brand15,16, Aaron M Wenger28, Maryam Ghareghani29,30,1, William T Harvey2, Benjamin Raeder4, Patrick Hasenfeld4, Allison A Regier31, Haley J Abel31, Ira M Hall32, Paul Flicek9, Oliver Stegle4,13, Mark B Gerstein18, Jose M C Tubio22,23, Zepeng Mu33, Yang I Li34, Xinghua Shi27, Alex R Hastie17, Kai Ye19,35, Zechen Chong20, Ashley D Sanders4, Michael C Zody26, Michael E Talkowski15,16, Ryan E Mills14,35, Scott E Devine24.
Abstract
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.Entities:
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Year: 2021 PMID： 33632895 PMCID： PMC8026704 DOI： 10.1126/science.abf7117
Source DB: PubMed Journal: Science ISSN： 0036-8075 Impact factor: 47.728