Literature DB >> 22543379

The 1000 Genomes Project: data management and community access.

Laura Clarke1, Xiangqun Zheng-Bradley, Richard Smith, Eugene Kulesha, Chunlin Xiao, Iliana Toneva, Brendan Vaughan, Don Preuss, Rasko Leinonen, Martin Shumway, Stephen Sherry, Paul Flicek.   

Abstract

The 1000 Genomes Project was launched as one of the largest distributed data collection and analysis projects ever undertaken in biology. In addition to the primary scientific goals of creating both a deep catalog of human genetic variation and extensive methods to accurately discover and characterize variation using new sequencing technologies, the project makes all of its data publicly available. Members of the project data coordination center have developed and deployed several tools to enable widespread data access.

Entities:  

Mesh：

Year:  2012        PMID： 22543379      PMCID： PMC3340611          DOI： 10.1038/nmeth.1974

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  14 in total

1.  Tabix: fast retrieval of sequence features from generic TAB-delimited files.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2011-01-05       Impact factor: 6.937

2.  Public data archives for genomic structural variation.

Authors:  Deanna M Church; Ilkka Lappalainen; Tam P Sneddon; Jonathan Hinton; Michael Maguire; John Lopez; John Garner; Justin Paschall; Michael DiCuccio; Eugene Yaschenko; Stephen W Scherer; Lars Feuk; Paul Flicek
Journal:  Nat Genet       Date:  2010-10       Impact factor: 38.330

3.  A map of human genome variation from population-scale sequencing.

Authors:  Gonçalo R Abecasis; David Altshuler; Adam Auton; Lisa D Brooks; Richard M Durbin; Richard A Gibbs; Matt E Hurles; Gil A McVean
Journal:  Nature       Date:  2010-10-28       Impact factor: 49.962

4.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

5.  Ensembl 2011.

Authors:  Paul Flicek; M Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Yuan Chen; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Leo Gordon; Maurice Hendrix; Thibaut Hourlier; Nathan Johnson; Andreas Kähäri; Damian Keefe; Stephen Keenan; Rhoda Kinsella; Felix Kokocinski; Eugene Kulesha; Pontus Larsson; Ian Longden; William McLaren; Bert Overduin; Bethan Pritchard; Harpreet Singh Riat; Daniel Rios; Graham R S Ritchie; Magali Ruffier; Michael Schuster; Daniel Sobral; Giulietta Spudich; Y Amy Tang; Stephen Trevanion; Jana Vandrovcova; Albert J Vilella; Simon White; Steven P Wilder; Amonida Zadissa; Jorge Zamora; Bronwen L Aken; Ewan Birney; Fiona Cunningham; Ian Dunham; Richard Durbin; Xosé M Fernández-Suarez; Javier Herrero; Tim J P Hubbard; Anne Parker; Glenn Proctor; Jan Vogel; Stephen M J Searle
Journal:  Nucleic Acids Res       Date:  2010-11-02       Impact factor: 16.971

6.  Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.

Authors:  William McLaren; Bethan Pritchard; Daniel Rios; Yuan Chen; Paul Flicek; Fiona Cunningham
Journal:  Bioinformatics       Date:  2010-06-18       Impact factor: 6.937

7.  The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.

Authors:  Nicole L Washington; E O Stinson; Marc D Perry; Peter Ruzanov; Sergio Contrino; Richard Smith; Zheng Zha; Rachel Lyne; Adrian Carr; Paul Lloyd; Ellen Kephart; Sheldon J McKay; Gos Micklem; Lincoln D Stein; Suzanna E Lewis
Journal:  Database (Oxford)       Date:  2011-08-19       Impact factor: 3.451

8.  The variant call format and VCFtools.

Authors:  Petr Danecek; Adam Auton; Goncalo Abecasis; Cornelis A Albers; Eric Banks; Mark A DePristo; Robert E Handsaker; Gerton Lunter; Gabor T Marth; Stephen T Sherry; Gilean McVean; Richard Durbin
Journal:  Bioinformatics       Date:  2011-06-07       Impact factor: 6.937

9.  Archiving next generation sequencing data.

Authors:  Martin Shumway; Guy Cochrane; Hideaki Sugawara
Journal:  Nucleic Acids Res       Date:  2009-12-03       Impact factor: 16.971

10.  ENCODE whole-genome data in the UCSC Genome Browser.

Authors:  Kate R Rosenbloom; Timothy R Dreszer; Michael Pheasant; Galt P Barber; Laurence R Meyer; Andy Pohl; Brian J Raney; Ting Wang; Angie S Hinrichs; Ann S Zweig; Pauline A Fujita; Katrina Learned; Brooke Rhead; Kayla E Smith; Robert M Kuhn; Donna Karolchik; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2009-11-17       Impact factor: 16.971
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  117 in total

1.  Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses.

Authors:  Shaunna L Clark; Joseph L McClay; Daniel E Adkins; Karolina A Aberg; Gaurav Kumar; Sri Nerella; Linying Xie; Ann L Collins; James J Crowley; Corey R Quakenbush; Christopher E Hillard; Guimin Gao; Andrey A Shabalin; Roseann E Peterson; William E Copeland; Judy L Silberg; Hermine Maes; Patrick F Sullivan; Elizabeth J Costello; Edwin J van den Oord
Journal:  Nicotine Tob Res       Date:  2015-08-17       Impact factor: 4.244

Review 2.  Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

Authors:  Khader Shameer; Lokesh P Tripathi; Krishna R Kalari; Joel T Dudley; Ramanathan Sowdhamini
Journal:  Brief Bioinform       Date:  2015-10-22       Impact factor: 11.622

Review 3.  Next-generation sequencing data interpretation: enhancing reproducibility and accessibility.

Authors:  Anton Nekrutenko; James Taylor
Journal:  Nat Rev Genet       Date:  2012-09       Impact factor: 53.242

4.  Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence.

Authors:  Shaunna L Clark; Joseph L McClay; Daniel E Adkins; Gaurav Kumar; Karolina A Aberg; Srilaxmi Nerella; Linying Xie; Ann L Collins; James J Crowley; Corey R Quackenbush; Christopher E Hilliard; Andrey A Shabalin; Scott I Vrieze; Roseann E Peterson; William E Copeland; Judy L Silberg; Matt McGue; Hermine Maes; William G Iacono; Patrick F Sullivan; Elizabeth J Costello; Edwin J van den Oord
Journal:  Alcohol Clin Exp Res       Date:  2017-03-24       Impact factor: 3.455

5.  New insights from existing sequence data: generating breakthroughs without a pipette.

Authors:  Alex M Plocik; Brenton R Graveley
Journal:  Mol Cell       Date:  2013-02-21       Impact factor: 17.970

6.  A fast and accurate method for detection of IBD shared haplotypes in genome-wide SNP data.

Authors:  Douglas W Bjelland; Uday Lingala; Piyush S Patel; Matt Jones; Matthew C Keller
Journal:  Eur J Hum Genet       Date:  2017-02-08       Impact factor: 4.246

7.  Effects of the absence of apolipoprotein e on lipoproteins, neurocognitive function, and retinal function.

Authors:  Angel C Y Mak; Clive R Pullinger; Ling Fung Tang; Jinny S Wong; Rahul C Deo; Jean-Marc Schwarz; Alejandro Gugliucci; Irina Movsesyan; Brian Y Ishida; Catherine Chu; Annie Poon; Phillip Kim; Eveline O Stock; Ernst J Schaefer; Bela F Asztalos; Joseph M Castellano; Tony Wyss-Coray; Jacque L Duncan; Bruce L Miller; John P Kane; Pui-Yan Kwok; Mary J Malloy
Journal:  JAMA Neurol       Date:  2014-10       Impact factor: 18.302

8.  Diversity of human tRNA genes from the 1000-genomes project.

Authors:  Marc Parisien; Xiaoyun Wang; Tao Pan
Journal:  RNA Biol       Date:  2013-12-09       Impact factor: 4.652

9.  Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases.

Authors:  Daniel Marbach; David Lamparter; Gerald Quon; Manolis Kellis; Zoltán Kutalik; Sven Bergmann
Journal:  Nat Methods       Date:  2016-03-07       Impact factor: 28.547

10.  Computational opportunities for remote collaboration and capacity building afforded by Web 2.0 and cloud computing.

Authors:  Willy Wriggers; Wilma K Olson; Cristobal G Dos Remedios
Journal:  Biophys Rev       Date:  2012-09-01
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