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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De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus
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TL;DR: Exome sequencing of 125 CH trios and 52 additional probands identified three genes with significant burden of rare damaging de novo or transmitted mutations and four genes required for neural tube development and regulate ventricular zone neural stem cell fate, implicate impaired neurogenesis in the pathogenesis of a subset of CH patients.
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Common risk variants identified in autism spectrum disorder
Jakob Grove,Stephan Ripke,Thomas Damm Als,Manuel Mattheisen,Raymond K. Walters,Hyejung Won,Jonatan Pallesen,Esben Agerbo,Ole A. Andreassen,Richard Anney,Rich Belliveau,Francesco Bettella,Joseph D. Buxbaum,Jonas Bybjerg-Grauholm,Marie Bækved-Hansen,Felecia Cerrato,Kimberly Chambert,Jane H. Christensen,Claire Churchhouse,Karin Dellenvall,Ditte Demontis,Silvia De Rubeis,Bernie Devlin,Srdjan Djurovic,Ashley Dumont,Jacqueline I. Goldstein,Christine Søholm Hansen,Mads E. Hauberg,Mads V. Hollegaard,Sigrun Hope,Daniel P. Howrigan,Hailiang Huang,Christina M. Hultman,Lambertus Klei,Julian Maller,Joanna Martin,Alicia R. Martin,Jennifer L. Moran,Mette Nyegaard,Terje Nærland,Duncan S. Palmer,Aarno Palotie,Carsten Bøcker Pedersen,Marianne Giørtz Pedersen,Timothy Poterba,Jesper Buchhave Poulsen,Beate St Pourcain,Per Qvist,Karola Rehnström,Avi Reichenberg,Jennifer Reichert,Elise B. Robinson,Kathryn Roeder,Panos Roussos,Evald Saemundsen,Sven Sandin,F. Kyle Satterstrom,George Davey Smith,Hreinn Stefansson,Kari Stefansson,Stacy Steinberg,Christine Stevens,Patrick F. Sullivan,Patrick Turley,G. Bragi Walters,Xinyi Xu,Bupgen,Bupgen,Daniel H. Geschwind,Merete Nordentoft,David M. Hougaard,Thomas Werge,Ole Mors,Preben Bo Mortensen,Benjamin M. Neale,Mark J. Daly,Anders D. Børglum +76 more
TL;DR: It is established that GWAS performed at scale will be much more productive in the near term in ASD, just as it has been in a broad range of important psychiatric and diverse medical phenotypes.
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A high-quality human reference panel reveals the complexity and distribution of genomic structural variants
Jayne Y. Hehir-Kwa,Tobias Marschall,Wigard P. Kloosterman,Laurent C. Francioli,Jasmijn A. Baaijens,Louis Dijkstra,Abdel Abdellaoui,Vyacheslav Koval,Djie Tjwan Thung,René Wardenaar,René Wardenaar,Ivo Renkens,Bradley P. Coe,Patrick Deelen,Joep de Ligt,Eric-Wubbo Lameijer,Freerk van Dijk,Fereydoun Hormozdiari,André G. Uitterlinden,Cornelia M. van Duijn,Evan E. Eichler,Paul I.W. de Bakker,Morris A. Swertz,Cisca Wijmenga,Gert-Jan B. van Ommen,P. Eline Slagboom,Dorret I. Boomsma,Alexander Schönhuth,Kai Ye,Kai Ye,Victor Guryev +30 more
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Microhaplotypes in forensic genetics
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Mapping And Phasing Of Structural Variation In Patient Genomes Using Nanopore Sequencing
Mircea Cretu Stancu,Markus J. van Roosmalen,Ivo Renkens,Marleen M. Nieboer,Sjors Middelkamp,Joep de Ligt,Giulia Pregno,Daniela Giachino,Giorgia Mandrile,Jose Espejo Valle-Inclan,Jerome Korzelius,Ewart de Bruijn,Edwin Cuppen,Michael E. Talkowski,Tobias Marschall,Jeroen de Ridder,Wigard P. Kloosterman +16 more
TL;DR: The value of long-read sequencing for screening whole genomes of patients for complex structural variants is demonstrated, using the ONT MinION at 11x and 16x mean coverage, for detection of de novo rearrangements originating from complex chromothripsis events in the patients.
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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.
Journal Article
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An integrated map of genetic variation from 1,092 human genomes
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TL;DR: It is shown that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites.
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