Literature DB >> 18852200

Practical aspects of imputation-driven meta-analysis of genome-wide association studies.

Paul I W de Bakker1, Manuel A R Ferreira, Xiaoming Jia, Benjamin M Neale, Soumya Raychaudhuri, Benjamin F Voight.   

Abstract

Motivated by the overwhelming success of genome-wide association studies, droves of researchers are working vigorously to exchange and to combine genetic data to expediently discover genetic risk factors for common human traits. The primary tools that fuel these new efforts are imputation, allowing researchers who have collected data on a diversity of genotype platforms to share data in a uniformly exchangeable format, and meta-analysis for pooling statistical support for a genotype-phenotype association. As many groups are forming collaborations to engage in these efforts, this review collects a series of guidelines, practical detail and learned experiences from a variety of individuals who have contributed to the subject.

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Year:  2008        PMID: 18852200      PMCID: PMC2782358          DOI: 10.1093/hmg/ddn288

Source DB:  PubMed          Journal:  Hum Mol Genet        ISSN: 0964-6906            Impact factor:   6.150


  40 in total

1.  Genomic control for association studies.

Authors:  B Devlin; K Roeder
Journal:  Biometrics       Date:  1999-12       Impact factor: 2.571

2.  A new multipoint method for genome-wide association studies by imputation of genotypes.

Authors:  Jonathan Marchini; Bryan Howie; Simon Myers; Gil McVean; Peter Donnelly
Journal:  Nat Genet       Date:  2007-06-17       Impact factor: 38.330

3.  Replicating genotype-phenotype associations.

Authors:  Stephen J Chanock; Teri Manolio; Michael Boehnke; Eric Boerwinkle; David J Hunter; Gilles Thomas; Joel N Hirschhorn; Goncalo Abecasis; David Altshuler; Joan E Bailey-Wilson; Lisa D Brooks; Lon R Cardon; Mark Daly; Peter Donnelly; Joseph F Fraumeni; Nelson B Freimer; Daniela S Gerhard; Chris Gunter; Alan E Guttmacher; Mark S Guyer; Emily L Harris; Josephine Hoh; Robert Hoover; C Augustine Kong; Kathleen R Merikangas; Cynthia C Morton; Lyle J Palmer; Elizabeth G Phimister; John P Rice; Jerry Roberts; Charles Rotimi; Margaret A Tucker; Kyle J Vogan; Sholom Wacholder; Ellen M Wijsman; Deborah M Winn; Francis S Collins
Journal:  Nature       Date:  2007-06-07       Impact factor: 49.962

4.  PLINK: a tool set for whole-genome association and population-based linkage analyses.

Authors:  Shaun Purcell; Benjamin Neale; Kathe Todd-Brown; Lori Thomas; Manuel A R Ferreira; David Bender; Julian Maller; Pamela Sklar; Paul I W de Bakker; Mark J Daly; Pak C Sham
Journal:  Am J Hum Genet       Date:  2007-07-25       Impact factor: 11.025

5.  New models of collaboration in genome-wide association studies: the Genetic Association Information Network.

Authors:  Teri A Manolio; Laura Lyman Rodriguez; Lisa Brooks; Gonçalo Abecasis; Dennis Ballinger; Mark Daly; Peter Donnelly; Stephen V Faraone; Kelly Frazer; Stacey Gabriel; Pablo Gejman; Alan Guttmacher; Emily L Harris; Thomas Insel; John R Kelsoe; Eric Lander; Norma McCowin; Matthew D Mailman; Elizabeth Nabel; James Ostell; Elizabeth Pugh; Stephen Sherry; Patrick F Sullivan; John F Thompson; James Warram; David Wholley; Patrice M Milos; Francis S Collins
Journal:  Nat Genet       Date:  2007-09       Impact factor: 38.330

6.  A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.

Authors:  Laura J Scott; Karen L Mohlke; Lori L Bonnycastle; Cristen J Willer; Yun Li; William L Duren; Michael R Erdos; Heather M Stringham; Peter S Chines; Anne U Jackson; Ludmila Prokunina-Olsson; Chia-Jen Ding; Amy J Swift; Narisu Narisu; Tianle Hu; Randall Pruim; Rui Xiao; Xiao-Yi Li; Karen N Conneely; Nancy L Riebow; Andrew G Sprau; Maurine Tong; Peggy P White; Kurt N Hetrick; Michael W Barnhart; Craig W Bark; Janet L Goldstein; Lee Watkins; Fang Xiang; Jouko Saramies; Thomas A Buchanan; Richard M Watanabe; Timo T Valle; Leena Kinnunen; Gonçalo R Abecasis; Elizabeth W Pugh; Kimberly F Doheny; Richard N Bergman; Jaakko Tuomilehto; Francis S Collins; Michael Boehnke
Journal:  Science       Date:  2007-04-26       Impact factor: 47.728

7.  Population structure and eigenanalysis.

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

8.  Imputation-based analysis of association studies: candidate regions and quantitative traits.

Authors:  Bertrand Servin; Matthew Stephens
Journal:  PLoS Genet       Date:  2007-05-30       Impact factor: 5.917

9.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.

Authors: 
Journal:  Nature       Date:  2007-06-07       Impact factor: 49.962

10.  Heterogeneity in meta-analyses of genome-wide association investigations.

Authors:  John P A Ioannidis; Nikolaos A Patsopoulos; Evangelos Evangelou
Journal:  PLoS One       Date:  2007-09-05       Impact factor: 3.240

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  316 in total

1.  Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.

Authors:  Eli A Stahl; Soumya Raychaudhuri; Elaine F Remmers; Gang Xie; Stephen Eyre; Brian P Thomson; Yonghong Li; Fina A S Kurreeman; Alexandra Zhernakova; Anne Hinks; Candace Guiducci; Robert Chen; Lars Alfredsson; Christopher I Amos; Kristin G Ardlie; Anne Barton; John Bowes; Elisabeth Brouwer; Noel P Burtt; Joseph J Catanese; Jonathan Coblyn; Marieke J H Coenen; Karen H Costenbader; Lindsey A Criswell; J Bart A Crusius; Jing Cui; Paul I W de Bakker; Philip L De Jager; Bo Ding; Paul Emery; Edward Flynn; Pille Harrison; Lynne J Hocking; Tom W J Huizinga; Daniel L Kastner; Xiayi Ke; Annette T Lee; Xiangdong Liu; Paul Martin; Ann W Morgan; Leonid Padyukov; Marcel D Posthumus; Timothy R D J Radstake; David M Reid; Mark Seielstad; Michael F Seldin; Nancy A Shadick; Sophia Steer; Paul P Tak; Wendy Thomson; Annette H M van der Helm-van Mil; Irene E van der Horst-Bruinsma; C Ellen van der Schoot; Piet L C M van Riel; Michael E Weinblatt; Anthony G Wilson; Gert Jan Wolbink; B Paul Wordsworth; Cisca Wijmenga; Elizabeth W Karlson; Rene E M Toes; Niek de Vries; Ann B Begovich; Jane Worthington; Katherine A Siminovitch; Peter K Gregersen; Lars Klareskog; Robert M Plenge
Journal:  Nat Genet       Date:  2010-05-09       Impact factor: 38.330

2.  Replication in genome-wide association studies.

Authors:  Peter Kraft; Eleftheria Zeggini; John P A Ioannidis
Journal:  Stat Sci       Date:  2009-11-01       Impact factor: 2.901

3.  Principal-component analysis for assessment of population stratification in mitochondrial medical genetics.

Authors:  Alessandro Biffi; Christopher D Anderson; Michael A Nalls; Rosanna Rahman; Akshata Sonni; Lynelle Cortellini; Natalia S Rost; Mar Matarin; Dena G Hernandez; Anna Plourde; Paul I W de Bakker; Owen A Ross; Steven M Greenberg; Karen L Furie; James F Meschia; Andrew B Singleton; Richa Saxena; Jonathan Rosand
Journal:  Am J Hum Genet       Date:  2010-05-27       Impact factor: 11.025

4.  Performance of genotype imputations using data from the 1000 Genomes Project.

Authors:  Yun Ju Sung; Lihua Wang; Tuomo Rankinen; Claude Bouchard; D C Rao
Journal:  Hum Hered       Date:  2011-12-30       Impact factor: 0.444

5.  Partial support for ZNF804A genotype-dependent alterations in prefrontal connectivity.

Authors:  Frieder M Paulus; Sören Krach; Johannes Bedenbender; Martin Pyka; Jens Sommer; Axel Krug; Susanne Knake; Markus M Nöthen; Stephanie H Witt; Marcella Rietschel; Tilo Kircher; Andreas Jansen
Journal:  Hum Brain Mapp       Date:  2011-10-31       Impact factor: 5.038

6.  Mapping rare and common causal alleles for complex human diseases.

Authors:  Soumya Raychaudhuri
Journal:  Cell       Date:  2011-09-30       Impact factor: 41.582

Review 7.  Genetic architectures of psychiatric disorders: the emerging picture and its implications.

Authors:  Patrick F Sullivan; Mark J Daly; Michael O'Donovan
Journal:  Nat Rev Genet       Date:  2012-07-10       Impact factor: 53.242

8.  Genome-wide association study identifies novel loci for plasma levels of protein C: the ARIC study.

Authors:  Weihong Tang; Saonli Basu; Xiaoxiao Kong; James S Pankow; Nena Aleksic; Adrian Tan; Mary Cushman; Eric Boerwinkle; Aaron R Folsom
Journal:  Blood       Date:  2010-08-27       Impact factor: 22.113

9.  Imputation aware meta-analysis of genome-wide association studies.

Authors:  Noah Zaitlen; Eleazar Eskin
Journal:  Genet Epidemiol       Date:  2010-09       Impact factor: 2.135

10.  Genome-wide association analysis identifies multiple loci related to resting heart rate.

Authors:  Mark Eijgelsheim; Christopher Newton-Cheh; Nona Sotoodehnia; Paul I W de Bakker; Martina Müller; Alanna C Morrison; Albert V Smith; Aaron Isaacs; Serena Sanna; Marcus Dörr; Pau Navarro; Christian Fuchsberger; Ilja M Nolte; Eco J C de Geus; Karol Estrada; Shih-Jen Hwang; Joshua C Bis; Ina-Maria Rückert; Alvaro Alonso; Lenore J Launer; Jouke Jan Hottenga; Fernando Rivadeneira; Peter A Noseworthy; Kenneth M Rice; Siegfried Perz; Dan E Arking; Tim D Spector; Jan A Kors; Yurii S Aulchenko; Kirill V Tarasov; Georg Homuth; Sarah H Wild; Fabio Marroni; Christian Gieger; Carmilla M Licht; Ronald J Prineas; Albert Hofman; Jerome I Rotter; Andrew A Hicks; Florian Ernst; Samer S Najjar; Alan F Wright; Annette Peters; Ervin R Fox; Ben A Oostra; Heyo K Kroemer; David Couper; Henry Völzke; Harry Campbell; Thomas Meitinger; Manuela Uda; Jacqueline C M Witteman; Bruce M Psaty; H-Erich Wichmann; Tamara B Harris; Stefan Kääb; David S Siscovick; Yalda Jamshidi; André G Uitterlinden; Aaron R Folsom; Martin G Larson; James F Wilson; Brenda W Penninx; Harold Snieder; Peter P Pramstaller; Cornelia M van Duijn; Edward G Lakatta; Stephan B Felix; Vilmundur Gudnason; Arne Pfeufer; Susan R Heckbert; Bruno H Ch Stricker; Eric Boerwinkle; Christopher J O'Donnell
Journal:  Hum Mol Genet       Date:  2010-07-16       Impact factor: 6.150

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