An integrated map of structural variation in 2,504 human genomes
Peter H. Sudmant,Tobias Rausch,Eugene J. Gardner,Robert E. Handsaker,Robert E. Handsaker,Alexej Abyzov,John Huddleston,Yan Zhang,Kai Ye,Goo Jun,Goo Jun,Markus His Yang Fritz,Miriam K. Konkel,Ankit Malhotra,Adrian M. Stütz,Xinghua Shi,Francesco Paolo Casale,Jieming Chen,Fereydoun Hormozdiari,Gargi Dayama,Ken Chen,Maika Malig,Mark Chaisson,Klaudia Walter,Sascha Meiers,Seva Kashin,Seva Kashin,Erik Garrison,Adam Auton,Hugo Y. K. Lam,Xinmeng Jasmine Mu,Xinmeng Jasmine Mu,Can Alkan,Danny Antaki,Taejeong Bae,Eliza Cerveira,Peter S. Chines,Zechen Chong,Laura Clarke,Elif Dal,Li Ding,S. Emery,Xian Fan,Madhusudan Gujral,Fatma Kahveci,Jeffrey M. Kidd,Yu Kong,Eric-Wubbo Lameijer,Shane A. McCarthy,Paul Flicek,Richard A. Gibbs,Gabor T. Marth,Christopher E. Mason,Androniki Menelaou,Androniki Menelaou,Donna M. Muzny,Bradley J. Nelson,Amina Noor,Nicholas F. Parrish,Matthew Pendleton,Andrew Quitadamo,Benjamin Raeder,Eric E. Schadt,Mallory Romanovitch,Andreas Schlattl,Robert Sebra,Andrey A. Shabalin,Andreas Untergasser,Jerilyn A. Walker,Min Wang,Fuli Yu,Chengsheng Zhang,Jing Zhang,Xiangqun Zheng-Bradley,Wanding Zhou,Thomas Zichner,Jonathan Sebat,Mark A. Batzer,Steven A. McCarroll,Steven A. McCarroll,Ryan E. Mills,Mark Gerstein,Ali Bashir,Oliver Stegle,Scott E. Devine,Charles Lee,Evan E. Eichler,Jan O. Korbel +87 more
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In this paper, the authors describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which are constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations.Abstract:
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.read more
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Sa41genome-wide gene-environment analyses of depression and reported lifetime traumatic experiences in uk biobank
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Spatial Chromatin Architecture Alteration by Structural Variations in Human Genomes at Population Scale
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TL;DR: This genome-wide study assesses the critical impact of structural variants on the higher order organization of chromatin folding and provides unique insight into the mechanisms regulating gene transcription at the population scale.
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The Clinical Application of RNA Sequencing in Genetic Diagnosis of Mendelian Disorders
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TL;DR: It is found that trio-based approaches using HiFi are the current gold standard although chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data, and 6-7 Mbp of DNA are incorrectly orientated per haplotype irrespective of whether trio-free or trio- based approaches are employed.
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Multiomics dissection of molecular regulatory mechanisms underlying autoimmune-associated noncoding SNPs
Xiao-Feng Chen,Ming-Rui Guo,Yuan-Yuan Duan,Feng Jiang,Hao Wu,Shan-Shan Dong,Xiao-Rong Zhou,Hlaing Nwe Thynn,Cong-Cong Liu,Lin Zhang,Yan Guo,Tie-Lin Yang +11 more
TL;DR: This work prioritized functional noncoding SNPs with regulatory gene targets associated with 19 autoimmune diseases by incorporating hundreds of immune cell–specific multiomics data and found that 90.1% of target genes are regulated by distal SNPs involving several TFs, suggesting the importance of long-range chromatin interaction in autoimmune diseases.
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An integrated encyclopedia of DNA elements in the human genome
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A global reference for human genetic variation.
Adam Auton,Gonçalo R. Abecasis,David Altshuler,Richard Durbin,David R. Bentley,Aravinda Chakravarti,Andrew G. Clark,Peter Donnelly,Evan E. Eichler,Paul Flicek,Stacey Gabriel,Richard A. Gibbs,Eric D. Green,Matthew E. Hurles,Bartha Maria Knoppers,Jan O. Korbel,Eric S. Lander,Charles Lee,Hans Lehrach,Elaine R. Mardis,Gabor T. Marth,Gil McVean,Deborah A. Nickerson,Jeanette Schmidt,Stephen T. Sherry,Jun Wang,Richard K. Wilson,Eric Boerwinkle,Harsha Doddapaneni,Yi Han,Viktoriya Korchina,Christie Kovar,Sandra L. Lee,Donna M. Muzny,Jeffrey G. Reid,Yiming Zhu,Yuqi Chang,Qiang Feng,Qiang Feng,Xiaodong Fang,Xiaodong Fang,Xiaosen Guo,Xiaosen Guo,Min Jian,Min Jian,Hui Jiang,Hui Jiang,Xin Jin,Tianming Lan,Guoqing Li,Jingxiang Li,Yingrui Li,Shengmao Liu,Xiao Liu,Xiao Liu,Yao Lu,Xuedi Ma,Meifang Tang,Bo Wang,Guangbiao Wang,Honglong Wu,Renhua Wu,Xun Xu,Ye Yin,Dandan Zhang,Wenwei Zhang,Jiao Zhao,Meiru Zhao,Xiaole Zheng,Namrata Gupta,Neda Gharani,Lorraine Toji,Norman P. Gerry,Alissa M. Resch,Jonathan Barker,Laura Clarke,Laurent Gil,Sarah E. Hunt,Gavin Kelman,Eugene Kulesha,Rasko Leinonen,William M. McLaren,Rajesh Radhakrishnan,Asier Roa,Dmitriy Smirnov,Richard Smith,Ian Streeter,Anja Thormann,Iliana Toneva,Brendan Vaughan,Xiangqun Zheng-Bradley,Russell J. Grocock,Sean Humphray,Terena James,Zoya Kingsbury,Ralf Sudbrak,M. Albrecht,Vyacheslav Amstislavskiy,Tatiana A. Borodina,Matthias Lienhard,Florian Mertes,Marc Sultan,Bernd Timmermann,Marie-Laure Yaspo,Lucinda Fulton,Victor Ananiev,Zinaida Belaia,Dimitriy Beloslyudtsev,Nathan Bouk,Chao Chen,Deanna M. Church,Robert M. Cohen,Charles Cook,John Garner,Timothy Hefferon,Mikhail Kimelman,Chunlei Liu,John Lopez,Peter Meric,Chris O’Sullivan,Yuri Ostapchuk,Lon Phan,Sergiy Ponomarov,Valerie A. Schneider,Eugene Shekhtman,Karl Sirotkin,Douglas J. Slotta,Hua Zhang,Senduran Balasubramaniam,John Burton,Petr Danecek,Thomas M. Keane,Anja Kolb-Kokocinski,Shane A. McCarthy,James Stalker,Michael A. Quail,Christopher Davies,Jeremy Gollub,Teresa Webster,Brant Wong,Yiping Zhan,Christopher L. Campbell,Yu Kong,Anthony Marcketta,Fuli Yu,Lilian Antunes,Matthew N. Bainbridge,Aniko Sabo,Zhuoyi Huang,Lachlan J. M. Coin,Lin Fang,Lin Fang,Qibin Li,Zhenyu Li,Haoxiang Lin,Binghang Liu,Ruibang Luo,Haojing Shao,Haojing Shao,Yinlong Xie,Chen Ye,Chang Yu,Fan Zhang,Hancheng Zheng,Zhu Hongmei,Can Alkan,Elif Dal,Fatma Kahveci,Erik Garrison,Deniz Kural,Wan-Ping Lee,Wen Fung Leong,Michael Strömberg,Alistair Ward,Jiantao Wu,Mengyao Zhang,Mark J. Daly,Mark A. DePristo,Robert E. Handsaker,Robert E. Handsaker,Eric Banks,Gaurav Bhatia,Guillermo del Angel,Giulio Genovese,Heng Li,Seva Kashin,Seva Kashin,Steven A. McCarroll,Steven A. McCarroll,James Nemesh,Ryan Poplin,Seungtai Yoon,Jayon Lihm,Vladimir Makarov,Srikanth Gottipati,Alon Keinan,Juan L. Rodriguez-Flores,Tobias Rausch,Markus Hsi-Yang Fritz,Adrian M. Stütz,Kathryn Beal,Avik Datta,Javier Herrero,Graham R. S. Ritchie,Daniel R. Zerbino,Pardis C. 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TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
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An integrated map of genetic variation from 1,092 human genomes
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