Collection

The 1000 Genomes Project

From One Genome to 1000 and Beyond in 25 years

We celebrate the 25th anniversary of the launch of the Human Genome Project (HGP) with recognition for human genomics resources, from one genome to over one thousand genomes and beyond.

The 1000 Genomes Project began in 2007 with the goal of developing a comprehensive resource of human genetic variation across worldwide populations. Eight years later, we publish in this issue the final phase reports from this project, representing the most comprehensive assessment of human genetic variation across global populations to date.  The already established datasets have, since their launch, provided a foundational open resource that has enabled a wealth of robust genetic associations to disease as well as many key insights into population history and evolution.

The final phase 1000 Genomes Project publications represent not only the completion of this project, but also the culmination of a series of international collaborations stemming from the HGP, including the International HapMap Project, all focused on establishing open reference catalogues of genetic variation as a resource to the community.

We are pleased to present this Nature Collection of all the primary publications and related news and commentary on the International HapMap and 1000 Genomes Projects. 

- Orli Bahcall, Senior Editor, Nature

 

Podcast

Podcast on completion of 1000 Genomes Project with Gil McVean and NHGRI Director Eric Green. What has been achieved in the twenty-five years since the start of the Human Genome Project.

News & Comment

Research

  • Nature | Article | open

    Results for the final phase of the 1000 Genomes Project are presented including whole-genome sequencing, targeted exome sequencing, and genotyping on high-density SNP arrays for 2,504 individuals across 26 populations, providing a global reference data set to support biomedical genetics.

    • The 1000 Genomes Project Consortium
  • Nature | Article | open

    The Structural Variation Analysis Group of The 1000 Genomes Project reports an integrated structural variation map based on discovery and genotyping of eight major structural variation classes in 2,504 unrelated individuals from across 26 populations; structural variation is compared within and between populations and its functional impact is quantified.

    • 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
    • , The 1000 Genomes Project Consortium
    • , Ryan E. Mills
    • , Mark B. Gerstein
    • , Ali Bashir
    • , Oliver Stegle
    • , Scott E. Devine
    • , Charles Lee
    • , Evan E. Eichler
    •  &  Jan O. Korbel
  • Nature | Article | open

    This report from the 1000 Genomes Project describes the genomes of 1,092 individuals from 14 human populations, providing a resource for common and low-frequency variant analysis in individuals from diverse populations; hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites, can be found in each individual.

    • The 1000 Genomes Project Consortium
  • Nature | Article

    Harnessing information from whole genome sequencing in 185 individuals, this study generates a high-resolution map of copy number variants. Nucleotide resolution of the map facilitates analysis of structural variant distribution and identification of the mechanisms of their origin. The study provides a resource for sequence-based association studies.

    • Ryan E. Mills
    • , Klaudia Walter
    • , Chip Stewart
    • , Robert E. Handsaker
    • , Ken Chen
    • , Can Alkan
    • , Alexej Abyzov
    • , Seungtai Chris Yoon
    • , Kai Ye
    • , R. Keira Cheetham
    • , Asif Chinwalla
    • , Donald F. Conrad
    • , Yutao Fu
    • , Fabian Grubert
    • , Iman Hajirasouliha
    • , Fereydoun Hormozdiari
    • , Lilia M. Iakoucheva
    • , Zamin Iqbal
    • , Shuli Kang
    • , Jeffrey M. Kidd
    • , Miriam K. Konkel
    • , Joshua Korn
    • , Ekta Khurana
    • , Deniz Kural
    • , Hugo Y. K. Lam
    • , Jing Leng
    • , Ruiqiang Li
    • , Yingrui Li
    • , Chang-Yun Lin
    • , Ruibang Luo
    • , Xinmeng Jasmine Mu
    • , James Nemesh
    • , Heather E. Peckham
    • , Tobias Rausch
    • , Aylwyn Scally
    • , Xinghua Shi
    • , Michael P. Stromberg
    • , Adrian M. Stütz
    • , Alexander Eckehart Urban
    • , Jerilyn A. Walker
    • , Jiantao Wu
    • , Yujun Zhang
    • , Zhengdong D. Zhang
    • , Mark A. Batzer
    • , Li Ding
    • , Gabor T. Marth
    • , Gil McVean
    • , Jonathan Sebat
    • , Michael Snyder
    • , Jun Wang
    • , Kenny Ye
    • , Evan E. Eichler
    • , Mark B. Gerstein
    • , Matthew E. Hurles
    • , Charles Lee
    • , Steven A. McCarroll
    • , Jan O. Korbel
    •  &  1000 Genomes Project
  • Nature | Article | open

    The goal of the 1000 Genomes Project is to provide in-depth information on variation in human genome sequences. In the pilot phase reported here, different strategies for genome-wide sequencing, using high-throughput sequencing platforms, were developed and compared. The resulting data set includes more than 95% of the currently accessible variants found in any individual, and can be used to inform association and functional studies.

    • The 1000 Genomes Project Consortium
  • Nature Communications | Article

    1000 Genomes imputation can increase the power of genome-wide association studies to detect genetic variants associated with human traits and diseases. Here, the authors develop a method to integrate and analyse low-coverage sequence data and SNP array data, and show that it improves imputation performance.

    • Olivier Delaneau
    • , Jonathan Marchini
    • , The 1000 Genomes Project Consortium
    • , Gil A. McVean
    • , Peter Donnelly
    • , Gerton Lunter
    • , Jonathan L. Marchini
    • , Simon Myers
    • , Anjali Gupta-Hinch
    • , Zamin Iqbal
    • , Iain Mathieson
    • , Andy Rimmer
    • , Dionysia K. Xifara
    • , Angeliki Kerasidou
    • , Claire Churchhouse
    • , Olivier Delaneau
    • , David M. Altshuler
    • , Stacey B. Gabriel
    • , Eric S. Lander
    • , Namrata Gupta
    • , Mark J. Daly
    • , Mark A. DePristo
    • , Eric Banks
    • , Gaurav Bhatia
    • , Mauricio O. Carneiro
    • , Guillermo del Angel
    • , Giulio Genovese
    • , Robert E. Handsaker
    • , Chris Hart
    • , Steven A. McCarroll
    • , James C. Nemesh
    • , Ryan E. Poplin
    • , Stephen F. Schaffner
    • , Khalid Shakir
    • , Pardis C. Sabeti
    • , Sharon R. Grossman
    • , Shervin Tabrizi
    • , Ridhi Tariya
    • , Heng Li
    • , David Reich
    • , Richard M. Durbin
    • , Matthew E. Hurles
    • , Senduran Balasubramaniam
    • , John Burton
    • , Petr Danecek
    • , Thomas M. Keane
    • , Anja Kolb-Kokocinski
    • , Shane McCarthy
    • , James Stalker
    • , Michael Quail
    • , Qasim Ayub
    • , Yuan Chen
    • , Alison J. Coffey
    • , Vincenza Colonna
    • , Ni Huang
    • , Luke Jostins
    • , Aylwyn Scally
    • , Klaudia Walter
    • , Yali Xue
    • , Yujun Zhang
    • , Ben Blackburne
    • , Sarah J. Lindsay
    • , Zemin Ning
    • , Adam Frankish
    • , Jennifer Harrow
    • , Chris Tyler-Smith
    • , Gonalo R. Abecasis
    • , Hyun Min Kang
    • , Paul Anderson
    • , Tom Blackwell
    • , Fabio Busonero
    • , Christian Fuchsberger
    • , Goo Jun
    • , Andrea Maschio
    • , Eleonora Porcu
    • , Carlo Sidore
    • , Adrian Tan
    • , Mary Kate Trost
    • , David R. Bentley
    • , Russell Grocock
    • , Sean Humphray
    • , Terena James
    • , Zoya Kingsbury
    • , Markus Bauer
    • , R. Keira Cheetham
    • , Tony Cox
    • , Michael Eberle
    • , Lisa Murray
    • , Richard Shaw
    • , Aravinda Chakravarti
    • , Andrew G. Clark
    • , Alon Keinan
    • , Juan L. Rodriguez-Flores
    • , Francisco M. De La Vega
    • , Jeremiah Degenhardt
    • , Evan E. Eichler
    • , Paul Flicek
    • , Laura Clarke
    • , Rasko Leinonen
    • , Richard E. Smith
    • , Xiangqun Zheng-Bradley
    • , Kathryn Beal
    • , Fiona Cunningham
    • , Javier Herrero
    • , William M. McLaren
    • , Graham R. S. Ritchie
    • , Jonathan Barker
    • , Gavin Kelman
    • , Eugene Kulesha
    • , Rajesh Radhakrishnan
    • , Asier Roa
    • , Dmitriy Smirnov
    • , Ian Streeter
    • , Iliana Toneva
    • , Richard A. Gibbs
    • , Huyen Dinh
    • , Christie Kovar
    • , Sandra Lee
    • , Lora Lewis
    • , Donna Muzny
    • , Jeff Reid
    • , Min Wang
    • , Fuli Yu
    • , Matthew Bainbridge
    • , Danny Challis
    • , Uday S. Evani
    • , James Lu
    • , Uma Nagaswamy
    • , Aniko Sabo
    • , Yi Wang
    • , Jin Yu
    • , Gerald Fowler
    • , Walker Hale
    • , Divya Kalra
    • , Eric D. Green
    • , Bartha M. Knoppers
    • , Jan O. Korbel
    • , Tobias Rausch
    • , Adrian M. Sttz
    • , Charles Lee
    • , Lauren Griffin
    • , Chih-Heng Hsieh
    • , Ryan E. Mills
    • , Marcin von Grotthuss
    • , Chengsheng Zhang
    • , Xinghua Shi
    • , Hans Lehrach
    • , Ralf Sudbrak
    • , Vyacheslav S. Amstislavskiy
    • , Matthias Lienhard
    • , Florian Mertes
    • , Marc Sultan
    • , Bernd Timmermann
    • , Marie-Laure Yaspo
    • , Sudbrak
    • , Ralf Herwig
    • , Elaine R. Mardis
    • , Richard K. Wilson
    • , Lucinda Fulton
    • , Robert Fulton
    • , George M. Weinstock
    • , Asif Chinwalla
    • , Li Ding
    • , David Dooling
    • , Daniel C. Koboldt
    • , Michael D. McLellan
    • , John W. Wallis
    • , Michael C. Wendl
    • , Qunyuan Zhang
    • , Gabor T. Marth
    • , Erik P. Garrison
    • , Deniz Kural
    • , Wan-Ping Lee
    • , Wen Fung Leong
    • , Alistair N. Ward
    • , Jiantao Wu
    • , Mengyao Zhang
    • , Deborah A. Nickerson
    • , Can Alkan
    • , Fereydoun Hormozdiari
    • , Arthur Ko
    • , Peter H. Sudmant
    • , Jeanette P. Schmidt
    • , Christopher J. Davies
    • , Jeremy Gollub
    • , Teresa Webster
    • , Brant Wong
    • , Yiping Zhan
    • , Stephen T. Sherry
    • , Chunlin Xiao
    • , Deanna Church
    • , Victor Ananiev
    • , Zinaida Belaia
    • , Dimitriy Beloslyudtsev
    • , Nathan Bouk
    • , Chao Chen
    • , Robert Cohen
    • , Charles Cook
    • , John Garner
    • , Timothy Hefferon
    • , Mikhail Kimelman
    • , Chunlei Liu
    • , John Lopez
    • , Peter Meric
    • , Yuri Ostapchuk
    • , Lon Phan
    • , Sergiy Ponomarov
    • , Valerie Schneider
    • , Eugene Shekhtman
    • , Karl Sirotkin
    • , Douglas Slotta
    • , Hua Zhang
    • , Jun Wang
    • , Xiaodong Fang
    • , Xiaosen Guo
    • , Min Jian
    • , Hui Jiang
    • , Xin Jin
    • , Guoqing Li
    • , Jingxiang Li
    • , Yingrui Li
    • , Xiao Liu
    • , Yao Lu
    • , Xuedi Ma
    • , Shuaishuai Tai
    • , Meifang Tang
    • , Bo Wang
    • , Guangbiao Wang
    • , Honglong Wu
    • , Renhua Wu
    • , Ye Yin
    • , Wenwei Zhang
    • , Jiao Zhao
    • , Meiru Zhao
    • , Xiaole Zheng
    • , Lachlan J.M. Coin
    • , Lin Fang
    • , Qibin Li
    • , Zhenyu Li
    • , Haoxiang Lin
    • , Binghang Liu
    • , Ruibang Luo
    • , Haojing Shao
    • , Bingqiang Wang
    • , Yinlong Xie
    • , Chen Ye
    • , Chang Yu
    • , Hancheng Zheng
    • , Hongmei Zhu
    • , Hongyu Cai
    • , Hongzhi Cao
    • , Yeyang Su
    • , Zhongming Tian
    • , Huanming Yang
    • , Ling Yang
    • , Jiayong Zhu
    • , Zhiming Cai
    • , Jian Wang
    • , Marcus W. Albrecht
    • , Tatiana A. Borodina
    • , Adam Auton
    • , Seungtai C. Yoon
    • , Jayon Lihm
    • , Vladimir Makarov
    • , Hanjun Jin
    • , Wook Kim
    • , Ki Cheol Kim
    • , Srikanth Gottipati
    • , Danielle Jones
    • , David N. Cooper
    • , Edward V. Ball
    • , Peter D. Stenson
    • , Bret Barnes
    • , Scott Kahn
    • , Kai Ye
    • , Mark A. Batzer
    • , Miriam K. Konkel
    • , Jerilyn A. Walker
    • , Daniel G. MacArthur
    • , Monkol Lek
    • , Mark D. Shriver
    • , Carlos D. Bustamante
    • , Simon Gravel
    • , Eimear E. Kenny
    • , Jeffrey M. Kidd
    • , Phil Lacroute
    • , Brian K. Maples
    • , Andres Moreno-Estrada
    • , Fouad Zakharia
    • , Brenna Henn
    • , Karla Sandoval
    • , Jake K. Byrnes
    • , Eran Halperin
    • , Yael Baran
    • , David W. Craig
    • , Alexis Christoforides
    • , Tyler Izatt
    • , Ahmet A. Kurdoglu
    • , Shripad A. Sinari
    • , Nils Homer
    • , Kevin Squire
    • , Jonathan Sebat
    • , Vineet Bafna
    • , Kenny Ye
    • , Esteban G. Burchard
    • , Ryan D. Hernandez
    • , Christopher R. Gignoux
    • , David Haussler
    • , Sol J. Katzman
    • , W. James Kent
    • , Bryan Howie
    • , Andres Ruiz-Linares
    • , Emmanouil T. Dermitzakis
    • , Tuuli Lappalainen
    • , Scott E. Devine
    • , Xinyue Liu
    • , Ankit Maroo
    • , Luke J. Tallon
    • , Jeffrey A. Rosenfeld
    • , Leslie P. Michelson
    • , Andrea Angius
    • , Francesco Cucca
    • , Serena Sanna
    • , Abigail Bigham
    • , Chris Jones
    • , Fred Reinier
    • , Yun Li
    • , Robert Lyons
    • , David Schlessinger
    • , Philip Awadalla
    • , Alan Hodgkinson
    • , Taras K. Oleksyk
    • , Juan C. Martinez-Cruzado
    • , Yunxin Fu
    • , Xiaoming Liu
    • , Momiao Xiong
    • , Lynn Jorde
    • , David Witherspoon
    • , Jinchuan Xing
    • , Brian L. Browning
    • , Iman Hajirasouliha
    • , Ken Chen
    • , Cornelis A. Albers
    • , Mark B. Gerstein
    • , Alexej Abyzov
    • , Jieming Chen
    • , Yao Fu
    • , Lukas Habegger
    • , Arif O. Harmanci
    • , Xinmeng Jasmine Mu
    • , Cristina Sisu
    • , Suganthi Balasubramanian
    • , Mike Jin
    • , Ekta Khurana
    • , Declan Clarke
    • , Jacob J. Michaelson
    • , Chris OSullivan
    • , Kathleen C. Barnes
    • , Neda Gharani
    • , Lorraine H. Toji
    • , Norman Gerry
    • , Jane S. Kaye
    • , Alastair Kent
    • , Rasika Mathias
    • , Pilar N. Ossorio
    • , Michael Parker
    • , Charles N. Rotimi
    • , Charmaine D. Royal
    • , Sarah Tishkoff
    • , Marc Via
    • , Walter Bodmer
    • , Gabriel Bedoya
    • , Gao Yang
    • , Chu Jia You
    • , Andres Garcia-Montero
    • , Alberto Orfao
    • , Julie Dutil
    • , Lisa D. Brooks
    • , Adam L. Felsenfeld
    • , Jean E. McEwen
    • , Nicholas C. Clemm
    • , Mark S. Guyer
    • , Jane L. Peterson
    • , Audrey Duncanson
    • , Michael Dunn
    •  &  Leena Peltonenz