Literature DB >> 19373277

Validating, augmenting and refining genome-wide association signals.

John P A Ioannidis1, Gilles Thomas, Mark J Daly.   

Abstract

Studies using genome-wide platforms have yielded an unprecedented number of promising signals of association between genomic variants and human traits. This Review addresses the steps required to validate, augment and refine such signals to identify underlying causal variants for well-defined phenotypes. These steps include: large-scale exact replication across both similar and diverse populations; fine mapping and resequencing; determination of the most informative markers and multiple independent informative loci; incorporation of functional information; and improved phenotype mapping of the implicated genetic effects. Even in cases for which replication proves that an effect exists, confident localization of the causal variant often remains elusive.

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Year:  2009        PMID: 19373277      PMCID: PMC7877552          DOI: 10.1038/nrg2544

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  115 in total

1.  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

2.  Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men.

Authors:  Matthew L Freedman; Christopher A Haiman; Nick Patterson; Gavin J McDonald; Arti Tandon; Alicja Waliszewska; Kathryn Penney; Robert G Steen; Kristin Ardlie; Esther M John; Ingrid Oakley-Girvan; Alice S Whittemore; Kathleen A Cooney; Sue A Ingles; David Altshuler; Brian E Henderson; David Reich
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-31       Impact factor: 11.205

Review 3.  Uncertainty in heterogeneity estimates in meta-analyses.

Authors:  John P A Ioannidis; Nikolaos A Patsopoulos; Evangelos Evangelou
Journal:  BMJ       Date:  2007-11-03

4.  Probability that a two-stage genome-wide association study will detect a disease-associated snp and implications for multistage designs.

Authors:  M H Gail; R M Pfeiffer; W Wheeler; D Pee
Journal:  Ann Hum Genet       Date:  2008-07-24       Impact factor: 1.670

5.  Genetic variation and activity of mouse Nod2, a susceptibility gene for Crohn's disease.

Authors:  Yasunori Ogura; Lisa Saab; Felicia F Chen; Adalberto Benito; Naohiro Inohara; Gabriel Nuñez
Journal:  Genomics       Date:  2003-04       Impact factor: 5.736

6.  Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24.

Authors:  Julius Gudmundsson; Patrick Sulem; Andrei Manolescu; Laufey T Amundadottir; Daniel Gudbjartsson; Agnar Helgason; Thorunn Rafnar; Jon T Bergthorsson; Bjarni A Agnarsson; Adam Baker; Asgeir Sigurdsson; Kristrun R Benediktsdottir; Margret Jakobsdottir; Jianfeng Xu; Thorarinn Blondal; Jelena Kostic; Jielin Sun; Shyamali Ghosh; Simon N Stacey; Magali Mouy; Jona Saemundsdottir; Valgerdur M Backman; Kristleifur Kristjansson; Alejandro Tres; Alan W Partin; Marjo T Albers-Akkers; Javier Godino-Ivan Marcos; Patrick C Walsh; Dorine W Swinkels; Sebastian Navarrete; Sarah D Isaacs; Katja K Aben; Theresa Graif; John Cashy; Manuel Ruiz-Echarri; Kathleen E Wiley; Brian K Suarez; J Alfred Witjes; Mike Frigge; Carole Ober; Eirikur Jonsson; Gudmundur V Einarsson; Jose I Mayordomo; Lambertus A Kiemeney; William B Isaacs; William J Catalona; Rosa B Barkardottir; Jeffrey R Gulcher; Unnur Thorsteinsdottir; Augustine Kong; Kari Stefansson
Journal:  Nat Genet       Date:  2007-04-01       Impact factor: 38.330

7.  Mutations in the human melanocortin-4 receptor gene associated with severe familial obesity disrupts receptor function through multiple molecular mechanisms.

Authors:  Giles S H Yeo; Emma J Lank; I Sadaf Farooqi; Julia Keogh; Benjamin G Challis; Stephen O'Rahilly
Journal:  Hum Mol Genet       Date:  2003-03-01       Impact factor: 6.150

Review 8.  Linkage disequilibrium--understanding the evolutionary past and mapping the medical future.

Authors:  Montgomery Slatkin
Journal:  Nat Rev Genet       Date:  2008-06       Impact factor: 53.242

9.  Cutting edge: autoimmune disease risk variant of STAT4 confers increased sensitivity to IFN-alpha in lupus patients in vivo.

Authors:  Silvia N Kariuki; Kyriakos A Kirou; Emma J MacDermott; Lilliana Barillas-Arias; Mary K Crow; Timothy B Niewold
Journal:  J Immunol       Date:  2009-01-01       Impact factor: 5.422

10.  Systematic identification of mammalian regulatory motifs' target genes and functions.

Authors:  Jason B Warner; Anthony A Philippakis; Savina A Jaeger; Fangxue Sherry He; Jolinta Lin; Martha L Bulyk
Journal:  Nat Methods       Date:  2008-03-02       Impact factor: 28.547

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  178 in total

1.  [Genetics of common chronic inflammatory skin diseases : An update on atopic dermatitis and psoriasis].

Authors:  E Rodríguez; K Eyerich; S Weidinger
Journal:  Hautarzt       Date:  2011-02       Impact factor: 0.751

2.  Consistency of genome-wide associations across major ancestral groups.

Authors:  Evangelia E Ntzani; George Liberopoulos; Teri A Manolio; John P A Ioannidis
Journal:  Hum Genet       Date:  2011-12-20       Impact factor: 4.132

3.  A flexible likelihood framework for detecting associations with secondary phenotypes in genetic studies using selected samples: application to sequence data.

Authors:  Dajiang J Liu; Suzanne M Leal
Journal:  Eur J Hum Genet       Date:  2011-12-14       Impact factor: 4.246

4.  Estimating the contribution of genetic variants to difference in incidence of disease between population groups.

Authors:  Ramal Moonesinghe; John P A Ioannidis; W Dana Flanders; Quanhe Yang; Benedict I Truman; Muin J Khoury
Journal:  Eur J Hum Genet       Date:  2012-02-15       Impact factor: 4.246

5.  2011 Presidential Address: from classroom to courtroom to clinic-closing the gaps in human genetics education.

Authors:  Lynn B Jorde
Journal:  Am J Hum Genet       Date:  2012-03-09       Impact factor: 11.025

6.  Linkage-disequilibrium-based binning affects the interpretation of GWASs.

Authors:  Andrea Christoforou; Michael Dondrup; Morten Mattingsdal; Manuel Mattheisen; Sudheer Giddaluru; Markus M Nöthen; Marcella Rietschel; Sven Cichon; Srdjan Djurovic; Ole A Andreassen; Inge Jonassen; Vidar M Steen; Pål Puntervoll; Stéphanie Le Hellard
Journal:  Am J Hum Genet       Date:  2012-03-22       Impact factor: 11.025

7.  Normal early pregnancy: a transient state of epigenetic change favoring hypomethylation.

Authors:  Wendy M White; Brian C Brost; Zhifu Sun; Carl Rose; Iasmina Craici; Steven J Wagner; Stephen Turner; Vesna D Garovic
Journal:  Epigenetics       Date:  2012-07-01       Impact factor: 4.528

8.  A meta-analysis of four genome-wide association studies of survival to age 90 years or older: the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium.

Authors:  Anne B Newman; Stefan Walter; Kathryn L Lunetta; Melissa E Garcia; P Eline Slagboom; Kaare Christensen; Alice M Arnold; Thor Aspelund; Yurii S Aulchenko; Emelia J Benjamin; Lene Christiansen; Ralph B D'Agostino; Annette L Fitzpatrick; Nora Franceschini; Nicole L Glazer; Vilmundur Gudnason; Albert Hofman; Robert Kaplan; David Karasik; Margaret Kelly-Hayes; Douglas P Kiel; Lenore J Launer; Kristin D Marciante; Joseph M Massaro; Iva Miljkovic; Michael A Nalls; Dena Hernandez; Bruce M Psaty; Fernando Rivadeneira; Jerome Rotter; Sudha Seshadri; Albert V Smith; Kent D Taylor; Henning Tiemeier; Hae-Won Uh; André G Uitterlinden; James W Vaupel; Jeremy Walston; Rudi G J Westendorp; Tamara B Harris; Thomas Lumley; Cornelia M van Duijn; Joanne M Murabito
Journal:  J Gerontol A Biol Sci Med Sci       Date:  2010-03-18       Impact factor: 6.053

9.  Multiple reciprocal adaptations and rapid genetic change upon experimental coevolution of an animal host and its microbial parasite.

Authors:  Rebecca D Schulte; Carsten Makus; Barbara Hasert; Nico K Michiels; Hinrich Schulenburg
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-05       Impact factor: 11.205

10.  Replication of past candidate loci for common diseases and phenotypes in 100 genome-wide association studies.

Authors:  Konstantinos C M Siontis; Nikolaos A Patsopoulos; John P A Ioannidis
Journal:  Eur J Hum Genet       Date:  2010-03-17       Impact factor: 4.246

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