1000 Genomes Edit

Citations: 2612

z-index: 653

Basic information
Short name 1000 Genomes
Full name 1000 Genomes
Description 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. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
URL http://browser.1000genomes.org
Year founded 2015
Last update & version
Availability Free to all users
Contact information

The contact information is provided to facilitate update of database information, and it is curated based on the contact details in the database or the related publications. To ensure effective contact with database constructors, we give priority to the contact details in the database.

University/Institution European Bioinformatics Institute
Address 7European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
City
Province/State
Country/Region United Kingdom
Contact name (PI/Team) Jan O. Korbel
Contact email (PI/Helpdesk) korbel@embl.de
Data information
Data object
Data type
Database category
Major organism
Keyword
Publications
  • An integrated map of structural variation in 2,504 human genomes. [PMID: 26432246]
    Peter H Sudmant, Tobias Rausch, Eugene J Gardner, Robert E Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-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 J P Chaisson, Klaudia Walter, Sascha Meiers, Seva Kashin, Erik Garrison, Adam Auton, Hugo Y K Lam, Xinmeng Jasmine Mu, Can Alkan, Danny Antaki, Taejeong Bae, Eliza Cerveira, Peter Chines, Zechen Chong, Laura Clarke, Elif Dal, Li Ding, Sarah Emery, Xian Fan, Madhusudan Gujral, Fatma Kahveci, Jeffrey M Kidd, Yu Kong, Eric-Wubbo Lameijer, Shane McCarthy, Paul Flicek, Richard A Gibbs, Gabor Marth, Christopher E Mason, 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, null null, Ryan E Mills, Mark B Gerstein, Ali Bashir, Oliver Stegle, Scott E Devine, Charles Lee, Evan E Eichler, Jan O Korbel

    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.

    Nature 2015:526(7571)

    386 Citations (from Europe PMC, 2019-05-18)

  • A global reference for human genetic variation. [PMID: 26432245]
    null null, Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis

    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. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

    Nature 2015:526(7571)

    2226 Citations (from Europe PMC, 2019-05-18)

Rank

  • Ranking in all databases: No. 5
  • Ranking in category/categories:
    • Gene genome and annotation: No. 4
    • Genotype phenotype and variation: No. 2
The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of 1000 Genomes.

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Record metadata

  • Created on: 2018-01-28
    • ***ok@***c.uk [2019-05-12]
    • ***d2011@***om [2019-05-10]
    • ***ina@***c.cn [2018-06-06]
    • ***imabatool@***u.edu.pk [2018-04-11]
    • ***ngyang17m@***c.cn [2018-01-27]

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