Phenotype harmonization and cross-study collaboration in GWAS consortia: The GENEVA experience

Genetic Epidemiology

Volumn 35, Issue 3, 2011, Pages 159-173

  Bennett, Siiri N ^a   Caporaso, Neil ^b   Fitzpatrick, Annette L ^a   Agrawal, Arpana ^c   Barnes, Kathleen ^d   Boyd, Heather A ^e   Cornelis, Marilyn C ^f   Hansel, Nadia N ^d   Heiss, Gerardo ^g   Heit, John A ^h   Kang, Jae Hee ⁱ   Kittner, Steven J ^j   Kraft, Peter ^f   Lowe, William ^k   Marazita, Mary L ^l,m,n   Monroe, Kristine R ^o   Pasquale, Louis R ⁱ   Ramos, Erin M ^p   van Dam, Rob M ^f,q   Udren, Jenna ^a   Williams, Kayleen ^a   more..

^a UNIVERSITY OF WASHINGTON   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e STATENS SERUM INSTITUT   (Denmark)

^f HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^g The University of North Carolina at Chapel Hill   (United States)

^h MAYO CLINIC   (United States)

ⁱ HARVARD MEDICAL SCHOOL   (United States)

^j UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^k NORTHWESTERN UNIVERSITY   (United States)

^l UNIVERSITY OF PITTSBURGH   (United States)

^m UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

ⁿ UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^o UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^p NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^q NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

more..

Author keywords

Consortia; GENEVA; Genome wide association studies; Harmonization; Phenotype

Indexed keywords

ALGORITHM; ARTICLE; ENVIRONMENT; FEASIBILITY STUDY; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; INFORMATION PROCESSING; PHENOTYPE; SAMPLE SIZE;

CASE-CONTROL STUDIES; COOPERATIVE BEHAVIOR; DATA COLLECTION; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; ENVIRONMENT; FEMALE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALE; MOLECULAR EPIDEMIOLOGY; PHENOTYPE; SAMPLE SIZE;

EID: 79952503255     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20564     Document Type: Article

References (31)

1. Browning BL, Browning SR. 2009. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84:210-223.
2. Cornelis MC, Agrawal A, Cole JW, Hansel NN, Barnes KC, Beaty TH, Bennett SN, Bierut LJ, Boerwinkle E, Doheny KF, Feenstra B, Feingold E, Fornage M, Haiman CA, Harris EL, Hayes MG, Heit JA, Hu FB, Kang JH, Laurie CC, Ling H, Manolio TA, Marazita ML, Mathias RA, Mirel DB, Paschall J, Pasquale LR, Pugh EW, Rice JP, Udren J, van Dam RM, Wang X, Wiggs JL, Williams K, Yu K for the GENEVA Consortium. 2010. The Gene, Environment Association Studies Consortium (GENEVA): maximizing the knowledge obtained from GWAS by collaboration across studies of multiple conditions. Genet Epidemiol 34:364-372.
3. Cornelis MC, Qi L, Kraft P, Hu FB. 2009. TCF7L2, dietary carbohydrate, and risk of type 2 diabetes in US women. Am J Clin Nutr 89:1256-1262.
4. de Bakker PIW, Ferreira MAR, Jia X, Neale BM, Raychaudhuri S, Voight BF. 2008. Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum Mol Genet 17:R122-R128.
5. Garcia-Closas M, Lubin JH. 1999. Power and sample size calculations in case-control studies of gene-environment interactions: comments on different approaches. Am J Epidemiol 149:689-692.
6. Goldstein DB. 2009. Common genetic variation and human traits. N Engl J Med 360:1696-1698.
7. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. PNAS 106:9362-9367.
8. Howie BN, Donnelly P, Marchini J. 2009. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5:e1000529.
9. International Schizophrenia Consortium, Purcell SM, Wray NR, Stone JL, Visscher PM, O'Donovan MC, Sullivan PF, Sklar P. 2009. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460:748-752.
10. Kang JH, Wiggs JL, Rosner BA, Hankinson SE, Abdrabou W, Fan BJ, Haines J, Pasquale LR. 2010. Endothelial nitric oxide synthase gene variants and primary open-angle glaucoma: interactions with sex and postmenopausal hormone use. Invest Ophthalmol Vis Sci 51:971-979.
11. Kraft P, Haiman CA. 2010. GWAS identifies a common breast cancer risk allele among BRCA1 carriers. Nat Genet 42:819-820.
12. Kraft P, Hunter D. 2005. Integrating epidemiology and genetic association: the challenge of gene-environment interaction. Phil Trans R Soc B 360:1609-1616.
13. Kraft P, Zeggini E, Ioannidis JPA. 2009. Replication in genome-wide association studies. Stat Sci 24:561-573.
14. Li Y, Abecasis GR. 2006. Mach 1.0: rapid haplotype reconstruction and missing genotype inference. Am J Hum Genet S79:2290.
15. Li Y, Willer C, Sanna S, Abecasis G. 2009. Genotype imputation. Annu Rev Genomics Hum Genet 10:387-406.
16. Lin DY, Sullivan PF. 2009. Meta-analysis of genome-wide association studies with overlapping subjects. Am J Hum Genet 85:862-872.
17. Lindgren CM, Heid IM, Randall JC, Lamina C, Steinthorsdottir V, Qi L, Speliotes EK, Thorleifsson G, Willer CJ, Herrera BM, Jackson AU, Lim N, Scheet P, Soranzo N, Amin N, Aulchenko YS, Chambers JC, Drong A, Luan J, Lyon HN, Rivadeneira F, Sanna S, Timpson NJ, Zillikens MC, Zhao JH, Almgren P, Bandinelli S, Bennett AJ, Bergman RN, Bonnycastle LL, Bumpstead SJ, Chanock SJ, Cherkas L, Chines P, Coin L, Cooper C, Crawford G, Doering A, Dominiczak A, Doney ASF, Ebrahim S, Elliott P, Erdos MR, Estrada K, Ferrucci L, Fischer G, Forouhi NG, Gieger C, Grallert H, Groves CJ, Grundy S, Guiducci C, Hadley D, Hamsten A, Havulinna AS, Hofman A, Holle R, Holloway JW, Illig T, Isomaa B, Jacobs LC, Jameson K, Jousilahti P, Karpe F, Kuusisto J, Laitinen J, Lathrop GM, Lawlor DA, Mangino M, McArdle WL, Meitinger T, Morken MA, Morris AP, Munroe P, Narisu N, Nordström A, Nordström P, Oostra BA, Palmer CNA, Payne F, Peden JF, Prokopenko I, Renström F, Ruokonen A, Salomaa V, Sandhu MS, Scott LJ, Scuteri A, Silander K, Song K, Yuan X, Stringham HM, Swift AJ, Tuomi T, Uda M, Vollenweider P, Waeber G, Wallace C, Walters GB, Weedon MN; The Wellcome Trust Case Control Consortium, Witteman JCM, Zhang C, Zhang W, Caulfield MJ, Collins FS, Smith GD, Day INM, Franks PW, Hattersley AT, Hu FB, Jarvelin MR, Kong A, Kooner JS, Laakso M, Lakatta E, Mooser V, Morris AD, Peltonen L, Samani NJ, Spector TD, Strachan DP, Tanaka T, Tuomilehto J, Uitterlinden AG, van Duijn CM, Wareham NJ, Watkins H for the PROCARDIS Consortia, Waterworth DM, Boehnke M, Deloukas P, Groop L, Hunter DJ, Thorsteinsdottir U, Schlessinger D, Wichmann HE, Frayling TM, Abecasis GR, Hirschhorn JN, Loos RJF, Stefansson K, Mohlke KL, Barroso I, McCarthy MI for the GIANT consortium. 2009. Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution. PLoS Genet 5:e1000508.
18. Lindström S, Yen YC, Spiegelman D, Kraft P. 2009. The impact of gene-environment dependence and misclassification in genetic association studies incorporating gene-environment interactions. Hum Hered 68:171-181.
19. Liu Y, Blackwood DH, Caesar S, de Geus EJC, Farmer A, Ferreira MAR, Ferrier IN, Fraser C, Gordon-Smith K, Green EK, Grozeva D, Gurling HM, Hamshere ML, Heutink P, Holmans PA, Hoogendijk WJ, Hottenga JJ, Jones L, Jones IR, Kirov G, Lin D, McGuffin P, Moskvina V, Nolen WA, Perlis RH, Posthuma D, Scolnick EM, Smit AB, Smit JH, Smoller JW, St Clair D, van Dyck R, Verhage M, Willemsen G, Young AH, Zandbelt T, Boomsma DI, Craddock N, O'Donovan MC, Owen MJ, Penninx BWJH, Purcell S, Sklar P, Sullivan PF, Wellcome Trust Case-Control Consortium. 2011. Meta-analysis of genome-wide association data of bipolar disorder and major depressive disorder. Mol Psychiatry 16:2-4.
20. Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, Bagoutdinov R, Hao L, Kiang A, Paschall J, Phan L, Popova N, Pretel S, Ziyabari L, Lee M, Shao Y, Wang ZY, Sirotkin K, Ward M, Kholodov M, Zbicz K, Beck J, Kimelman M, Shevelev S, Preuss D, Yaschenko E, Graeff A, Ostell J, Sherry ST. 2007. The NCBI dbGaP database of genotypes and phenotypes. Nat Genet 39:1181-1186.
21. Manolio TA, Rodriguez LL, Brooks L, Abecasis G, the Collaborative Association Study of Psoriasis, Ballinger D, Daly M, Donnelly P, Faraone SV, the International Multi-Center ADHD Genetics Project, Frazer K, Gabriel S, Gejman P, the Molecular Genetics of Schizophrenia Collaboration, Guttmacher A, Harris EL, Insel T, Kelsoe JR, the Bipolar Genome Study, Lander E, McCowin N, Mailman MD, Nabel E, Ostell J, Pugh E, Sherry S, Sullivan PF, the Major Depression Stage 1 Genomewide Association in Population-Based Samples Study, Thompson JF, Warram J, the Genetics of Kidneys in Diabetes (GoKinD) Study, Wholley D, Milos PM, Collins FS. 2007. New models of collaboration in genome-wide association studies: the Genetic Association Information Network. Nat Genet 39:1045-1051.
22. Marchini J, Howie B, Myers S, McVean G, Donnelly P. 2007. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39:906-913.
23. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JPA, Hirschhorn JN. 2008. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature 9:356-369.
24. Psaty BM, O'Donnell CJ, Gudnason V, Lunetta KL, Folsom AR, Rotter JI, Uitterlinden AG, Harris TB, Witteman JCM, Boerwinkle E, on behalf of the CHARGE Consortium. 2009. Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium: design of prospective meta-analyses of genome-wide association studies from 5 cohorts. Circ Cardiovasc Genet 2:73-80.
25. Psychiatric GWAS Consortium Coordinating Committee, Cichon S, Craddock N, Daly M, Faraone SV, Gejman PV, Kelsoe J, Lehner T, Levinson DF, Moran A, Sklar P, Sullivan PF. 2009. Genomewide association studies: history, rationale, and prospects for psychiatric disorders. Am J Psychiatry 166:540-556.
26. Rimm EB, Stampfer MJ, Colditz GA, Chute CG, Litin LB, Willett WC. 1990. Validity of self-reported waist and hip circumferences in men and women. Epidemiology 1:466-473.
27. Seminara D, Khoury MJ, O'Brien TR, Manolio T, Gwinn ML, Little J, Higgins JPT, Bernstein JL, Boffetta P, Bondy M, Bray MS, Brenchley PE, Buffler PA, Casas JP, Chokkalingam AP, Danesh J, Smith GD, Dolan S, Duncan R, Gruis NA, Hashibe M, Hunter D, Jarvelin M-R, Malmer B, Maraganore DM, Newton-Bishop JA, Riboli E, Salanti G, Taioli E, Timpson N, Uitterlinden AG, Vineis P, Wareham N, Winn DM, Zimmern R, Ioannidis JPA for the Human Genome Epidemiology Network and the Network of Investigator Networks. 2007. The emergence of networks in human genome epidemiology: challenges and opportunities. Epidemiology 18:1-8.
28. Thorgeirsson TE, Gudbjartsson DF, Surakka I, Vink JM, Amin N, Geller F, Sulem P, Rafnar T, Esko T, Walter S, Gieger C, Rawal R, Mangino M, Prokopenko I, Mägi R, Keskitalo K, Gudjonsdottir IH, Gretarsdottir S, Stefansson H, Thompson JR, Aulchenko YS, Nelis M, Aben KK, den Heijer M, Dirksen A, Ashraf H, Soranzo N, Valdes AM, Steves C, Uitterlinden AG, Hofman A, Tönjes A, Kovacs P, Hottenga JJ, Willemsen G, Vogelzangs N, Döring A, Dahmen N, Nitz B, Pergadia ML, Saez B, De Diego V, Lezcano V, Garcia-Prats MD, Ripatti S, Perola M, Kettunen J, Hartikainen AL, Pouta A, Laitinen J, Isohanni M, Huei-Yi S, Allen M, Krestyaninova M, Hall AS, Jones GT, van Rij AM, Mueller T, Dieplinger B, Haltmayer M, Jonsson S, Matthiasson SE, Oskarsson H, Tyrfingsson T, Kiemeney LA, Mayordomo JI, Lindholt JS, Pedersen JH, Franklin WA, Wolf H, Montgomery GW, Heath AC, Martin NG, Madden PAF, Giegling I, Rujescu D, Järvelin MR, Salomaa V, Stumvoll M, Spector TD, Wichmann HE, Metspalu A, Samani NJ, Penninx BW, Oostra BA, Boomsma DI, Tiemeier H, van Duijn CM, Kaprio J, Gulcher JR, The ENGAGE Consortium, McCarthy MI, Peltonen L, Thorsteinsdottir U, Stefansson K. 2010. Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. Nat Genet 42:448-453.
29. Thorleifsson G, Walters GB, Hewitt AW, Masson G, Helgason A, DeWan A, Sigurdsson A, Jonasdottir A, Gudjonsson SA, Magnusson KP, Stefansson H, Lam DSC, Tam POS, Gudmundsdottir GJ, Southgate L, Burdon KP, Gottfredsdottir MS, Aldred MA, Mitchell P, St Clair D, Collier DA, Tang N, Sveinsson O, Macgregor S, Martin NG, Cree AJ, Gibson J, MacLeod A, Jacob A, Ennis S, Young TL, Chan JCN, Karwatowski WSS, Hammond CJ, Thordarson K, Zhang M, Wadelius C, Lotery AJ, Trembath RC, Pang CP, Hoh J, Craig JE, Kong A, Mackey DA, Jonasson F, Thorsteinsdottir U, Stefansson K. 2010. Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma. Nat Genet 42:906-909.
30. Wolfs RCW, Klaver CCW, Ramrattan RS, van Duijn CM, Hofman A, de Jong PTVM. 1998. Genetic risk of primary open-angle glaucoma. Arch Ophthalmol 116:1640-1645.
31. Zeggini E, Ioannidis JPA. 2009. Meta-analysis in genome-wide association studies. Pharmacogenomics 10:191-201.