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Literature DB >> 20560038

Genome-wide association studies--data generation, storage, interpretation, and bioinformatics.

Abstract

Genome-wide association studies (GWAS) have had great success in identifying common genetic determinants of disease. One of the challenges posed by GWAS is the analysis of the large amount of data generated. This review aims to provide the non-geneticists with an overview of the different steps entailed in analysis of GWAS data, with an emphasis on popular bioinformatics tools available. GWAS data generation, analysis, and interpretation will be covered.

Mesh：

Year: 2010 PMID： 20560038 DOI： 10.1007/s12265-010-9181-y

Source DB: PubMed Journal: J Cardiovasc Transl Res ISSN： 1937-5387 Impact factor: 4.132

44 in total

1. A note on exact tests of Hardy-Weinberg equilibrium.

Authors: Janis E Wigginton; David J Cutler; Goncalo R Abecasis
Journal: Am J Hum Genet Date: 2005-03-23 Impact factor: 11.025

2. A haplotype map of the human genome.

Authors:
Journal: Nature Date: 2005-10-27 Impact factor: 49.962

3. Principal components analysis corrects for stratification in genome-wide association studies.

Authors: Alkes L Price; Nick J Patterson; Robert M Plenge; Michael E Weinblatt; Nancy A Shadick; David Reich
Journal: Nat Genet Date: 2006-07-23 Impact factor: 38.330

4. GenABEL: an R library for genome-wide association analysis.

Authors: Yurii S Aulchenko; Stephan Ripke; Aaron Isaacs; Cornelia M van Duijn
Journal: Bioinformatics Date: 2007-03-23 Impact factor: 6.937

5. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

Authors: Lucia A Hindorff; Praveen Sethupathy; Heather A Junkins; Erin M Ramos; Jayashri P Mehta; Francis S Collins; Teri A Manolio
Journal: Proc Natl Acad Sci U S A Date: 2009-05-27 Impact factor: 11.205

6. SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap.

Authors: Andrew D Johnson; Robert E Handsaker; Sara L Pulit; Marcia M Nizzari; Christopher J O'Donnell; Paul I W de Bakker
Journal: Bioinformatics Date: 2008-10-30 Impact factor: 6.937

7. Discovery properties of genome-wide association signals from cumulatively combined data sets.

Authors: Tiago V Pereira; Nikolaos A Patsopoulos; Georgia Salanti; John P A Ioannidis
Journal: Am J Epidemiol Date: 2009-10-06 Impact factor: 4.897

8. Human non-synonymous SNPs: server and survey.

Authors: Vasily Ramensky; Peer Bork; Shamil Sunyaev
Journal: Nucleic Acids Res Date: 2002-09-01 Impact factor: 16.971

9. A second generation human haplotype map of over 3.1 million SNPs.

Authors: Kelly A Frazer; Dennis G Ballinger; David R Cox; David A Hinds; Laura L Stuve; Richard A Gibbs; John W Belmont; Andrew Boudreau; Paul Hardenbol; Suzanne M Leal; Shiran Pasternak; David A Wheeler; Thomas D Willis; Fuli Yu; Huanming Yang; Changqing Zeng; Yang Gao; Haoran Hu; Weitao Hu; Chaohua Li; Wei Lin; Siqi Liu; Hao Pan; Xiaoli Tang; Jian Wang; Wei Wang; Jun Yu; Bo Zhang; Qingrun Zhang; Hongbin Zhao; Hui Zhao; Jun Zhou; Stacey B Gabriel; Rachel Barry; Brendan Blumenstiel; Amy Camargo; Matthew Defelice; Maura Faggart; Mary Goyette; Supriya Gupta; Jamie Moore; Huy Nguyen; Robert C Onofrio; Melissa Parkin; Jessica Roy; Erich Stahl; Ellen Winchester; Liuda Ziaugra; David Altshuler; Yan Shen; Zhijian Yao; Wei Huang; Xun Chu; Yungang He; Li Jin; Yangfan Liu; Yayun Shen; Weiwei Sun; Haifeng Wang; Yi Wang; Ying Wang; Xiaoyan Xiong; Liang Xu; Mary M Y Waye; Stephen K W Tsui; Hong Xue; J Tze-Fei Wong; Luana M Galver; Jian-Bing Fan; Kevin Gunderson; Sarah S Murray; Arnold R Oliphant; Mark S Chee; Alexandre Montpetit; Fanny Chagnon; Vincent Ferretti; Martin Leboeuf; Jean-François Olivier; Michael S Phillips; Stéphanie Roumy; Clémentine Sallée; Andrei Verner; Thomas J Hudson; Pui-Yan Kwok; Dongmei Cai; Daniel C Koboldt; Raymond D Miller; Ludmila Pawlikowska; Patricia Taillon-Miller; Ming Xiao; Lap-Chee Tsui; William Mak; You Qiang Song; Paul K H Tam; Yusuke Nakamura; Takahisa Kawaguchi; Takuya Kitamoto; Takashi Morizono; Atsushi Nagashima; Yozo Ohnishi; Akihiro Sekine; Toshihiro Tanaka; Tatsuhiko Tsunoda; Panos Deloukas; Christine P Bird; Marcos Delgado; Emmanouil T Dermitzakis; Rhian Gwilliam; Sarah Hunt; Jonathan Morrison; Don Powell; Barbara E Stranger; Pamela Whittaker; David R Bentley; Mark J Daly; Paul I W de Bakker; Jeff Barrett; Yves R Chretien; Julian Maller; Steve McCarroll; Nick Patterson; Itsik Pe'er; Alkes Price; Shaun Purcell; Daniel J Richter; Pardis Sabeti; Richa Saxena; Stephen F Schaffner; Pak C Sham; Patrick Varilly; David Altshuler; Lincoln D Stein; Lalitha Krishnan; Albert Vernon Smith; Marcela K Tello-Ruiz; Gudmundur A Thorisson; Aravinda Chakravarti; Peter E Chen; David J Cutler; Carl S Kashuk; Shin Lin; Gonçalo R Abecasis; Weihua Guan; Yun Li; Heather M Munro; Zhaohui Steve Qin; Daryl J Thomas; Gilean McVean; Adam Auton; Leonardo Bottolo; Niall Cardin; Susana Eyheramendy; Colin Freeman; Jonathan Marchini; Simon Myers; Chris Spencer; Matthew Stephens; Peter Donnelly; Lon R Cardon; Geraldine Clarke; David M Evans; Andrew P Morris; Bruce S Weir; Tatsuhiko Tsunoda; James C Mullikin; Stephen T Sherry; Michael Feolo; Andrew Skol; Houcan Zhang; Changqing Zeng; Hui Zhao; Ichiro Matsuda; Yoshimitsu Fukushima; Darryl R Macer; Eiko Suda; Charles N Rotimi; Clement A Adebamowo; Ike Ajayi; Toyin Aniagwu; Patricia A Marshall; Chibuzor Nkwodimmah; Charmaine D M Royal; Mark F Leppert; Missy Dixon; Andy Peiffer; Renzong Qiu; Alastair Kent; Kazuto Kato; Norio Niikawa; Isaac F Adewole; Bartha M Knoppers; Morris W Foster; Ellen Wright Clayton; Jessica Watkin; Richard A Gibbs; John W Belmont; Donna Muzny; Lynne Nazareth; Erica Sodergren; George M Weinstock; David A Wheeler; Imtaz Yakub; Stacey B Gabriel; Robert C Onofrio; Daniel J Richter; Liuda Ziaugra; Bruce W Birren; Mark J Daly; David Altshuler; Richard K Wilson; Lucinda L Fulton; Jane Rogers; John Burton; Nigel P Carter; Christopher M Clee; Mark Griffiths; Matthew C Jones; Kirsten McLay; Robert W Plumb; Mark T Ross; Sarah K Sims; David L Willey; Zhu Chen; Hua Han; Le Kang; Martin Godbout; John C Wallenburg; Paul L'Archevêque; Guy Bellemare; Koji Saeki; Hongguang Wang; Daochang An; Hongbo Fu; Qing Li; Zhen Wang; Renwu Wang; Arthur L Holden; Lisa D Brooks; Jean E McEwen; Mark S Guyer; Vivian Ota Wang; Jane L Peterson; Michael Shi; Jack Spiegel; Lawrence M Sung; Lynn F Zacharia; Francis S Collins; Karen Kennedy; Ruth Jamieson; John Stewart
Journal: Nature Date: 2007-10-18 Impact factor: 49.962

10. Population structure and eigenanalysis.

Authors: Nick Patterson; Alkes L Price; David Reich
Journal: PLoS Genet Date: 2006-12 Impact factor: 5.917

8 in total

1. Gene set enrichment; a problem of pathways.

Authors: Matthew N Davies; Emma L Meaburn; Leonard C Schalkwyk
Journal: Brief Funct Genomics Date: 2010-09-22 Impact factor: 4.241

2. Molecular biology of heart disease.

Authors: Robert Roberts
Journal: World J Cardiol Date: 2011-04-26

3. The Rules of Variation Expanded, Implications for the Research on Compatible Genomics.

Authors: Fernando Castro-Chavez
Journal: Biosemiotics Date: 2011-05-12 Impact factor: 0.711

Review 4. Novel sequencing-based strategies for high-throughput discovery of genetic mutations underlying inherited antibody deficiency disorders.

Authors: Hong-Ying Wang; Ashish Jain
Journal: Curr Allergy Asthma Rep Date: 2011-10 Impact factor: 4.806

Review 5. Genome-wide association studies in Africans and African Americans: expanding the framework of the genomics of human traits and disease.

Authors: Emmanuel Peprah; Huichun Xu; Fasil Tekola-Ayele; Charmaine D Royal
Journal: Public Health Genomics Date: 2014-11-26 Impact factor: 2.000

Review 6. Systematic Molecular Phenotyping: A Path Toward Precision Emergency Medicine?

Authors: Alexander T Limkakeng; Andrew A Monte; Christopher Kabrhel; Michael Puskarich; Laura Heitsch; Ephraim L Tsalik; Nathan I Shapiro
Journal: Acad Emerg Med Date: 2016-10-03 Impact factor: 3.451

Review 7. Promises and challenges of pharmacogenetics: an overview of study design, methodological and statistical issues.

Authors: Stephanie Ross; Sonia S Anand; Philip Joseph; Guillaume Paré
Journal: JRSM Cardiovasc Dis Date: 2012-04-05

8. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.

Authors: Glenn T Howe; Jianbin Yu; Brian Knaus; Richard Cronn; Scott Kolpak; Peter Dolan; W Walter Lorenz; Jeffrey F D Dean
Journal: BMC Genomics Date: 2013-02-28 Impact factor: 3.969

8 in total