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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Copy Number Variations in Candidate Genes and Intergenic Regions Affect Body Mass Index and Abdominal Obesity in Mexican Children.
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TL;DR: The results indicate a possible contribution of CNVs in LEPR, NEGR1, ARHGEF4, and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d to the development of obesity, particularly abdominal obesity in Mexican children.
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Cytogenetically visible inversions are formed by multiple molecular mechanisms
Maria Pettersson,Maria Pettersson,Christopher M. Grochowski,Josephine Wincent,Josephine Wincent,Jesper Eisfeldt,Jesper Eisfeldt,Amy M. Breman,Sau Wai Cheung,Ana Cristina Victorino Krepischi,Carla Rosenberg,James R. Lupski,James R. Lupski,Jesper Ottosson,Lovisa Lovmar,Jelena Gacic,Elisabeth Syk Lundberg,Elisabeth Syk Lundberg,Daniel Nilsson,Daniel Nilsson,Daniel Nilsson,Claudia M.B. Carvalho,Claudia M.B. Carvalho,Anna Lindstrand,Anna Lindstrand +24 more
TL;DR: This study indicates that short‐read 30x coverage WGS can detect a substantial fraction of chromosomal inversions and finds that replication‐based mechanisms are responsible for approximately 38% of those events leading to a significant proportion of inversions that are actually accompanied by additional copy‐number variation potentially contributing to the overall phenotypic presentation of those patients.
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Genomic characterization of the adolescent idiopathic scoliosis associated transcriptome and regulome
Nadja Makki,Jingjing Zhao,Zhaoyang Liu,Walter L. Eckalbar,Aki Ushiki,Anas M. Khanshour,Joe Wu,Jonathan J. Rios,Jonathan J. Rios,Ryan S. Gray,Carol Wise,Carol Wise,Nadav Ahituv +12 more
TL;DR: This study defines the expression of AIS-associated genes and active regulatory elements by performing RNA-seq and chromatin immunoprecipitation-sequencing against H3 lysine 27 acetylation in tissues in mouse and human and identifies three functional enhancers carrying Ais-associated GWAS SNPs at the ADGRG6 and BNC2 loci.
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Medical Records-Based Genetic Studies of the Complement System.
Atlas Khan,Ning Shang,Lynn Petukhova,Jun Zhang,Yufeng Shen,Scott J. Hebbring,Halima Moncrieffe,Leah C. Kottyan,Bahram Namjou-Khales,Rachel Knevel,Soumya Raychaudhuri,Elizabeth W. Karlson,John B. Harley,Ian B. Stanaway,David R. Crosslin,Joshua C. Denny,Mitchell S.V. Elkind,Ali G. Gharavi,George Hripcsak,Chunhua Weng,Krzysztof Kiryluk +20 more
TL;DR: In this article, the authors performed medical records-based genome-wide and phenome-wide association studies for plasma C3 and C4 levels among participants of the eMERGE network.
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A framework to score the effects of structural variants in health and disease
Philip Kleinert,Martin Kircher +1 more
TL;DR: CADD-SV is described, a method to retrieve and integrate a wide set of annotations to predict the effects of SVs, and it is shown that it can prioritize somatic cancer variants as well as noncoding variants known to affect gene expression.
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An integrated encyclopedia of DNA elements in the human genome
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Journal ArticleDOI
A global reference for human genetic variation.
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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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