Journal article
Phenotype harmonization and cross-study collaboration in GWAS consortia: the GENEVA experience
Genetic epidemiology, Vol.35(3), pp.159-173
04/2011
DOI: 10.1002/gepi.20564
PMCID: PMC3055921
PMID: 21284036
Abstract
Genome-wide association study (GWAS) consortia and collaborations formed
to detect genetic loci for common phenotypes or investigate gene-environment
(G*E) interactions are increasingly common. While these consortia
effectively increase sample size, phenotype heterogeneity across studies
represents a major obstacle that limits successful identification of these
associations. Investigators are faced with the challenge of how to harmonize
previously collected phenotype data obtained using different data collection
instruments which cover topics in varying degrees of detail and over diverse
time frames. This process has not been described in detail. We describe here
some of the strategies and pitfalls associated with combining phenotype data
from varying studies. Using the Gene Environment Association Studies (GENEVA)
multi-site GWAS consortium as an example, this paper provides an illustration to
guide GWAS consortia through the process of phenotype harmonization and
describes key issues that arise when sharing data across disparate studies.
GENEVA is unusual in the diversity of disease endpoints and so the issues it
faces as its participating studies share data will be informative for many
collaborations. Phenotype harmonization requires identifying common phenotypes,
determining the feasibility of cross-study analysis for each, preparing common
definitions, and applying appropriate algorithms. Other issues to be considered
include genotyping timeframes, coordination of parallel efforts by other
collaborative groups, analytic approaches, and imputation of genotype data.
GENEVA's harmonization efforts and policy of promoting data sharing and
collaboration, not only within GENEVA but also with outside collaborations, can
provide important guidance to ongoing and new consortia.
Details
- Title: Subtitle
- Phenotype harmonization and cross-study collaboration in GWAS consortia: the GENEVA experience
- Creators
- Siiri N Bennett - Collaborative Health Studies Coordinating Center, Department of Biostatistics, University of Washington, Seattle, WANeil Caporaso - Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MDAnnette L Fitzpatrick - Collaborative Health Studies Coordinating Center, Department of Biostatistics, University of Washington, Seattle, WAArpana Agrawal - Department of Psychiatry, Washington University School of Medicine, Saint Louis, MOKathleen Barnes - Johns Hopkins University School of Medicine, Baltimore, MDHeather A Boyd - Department of Epidemiology Research, Statens Serum Institut, Copenhagen, DenmarkMarilyn C Cornelis - Harvard School of Public Health, Boston, MANadia N Hansel - Johns Hopkins University School of Medicine, Baltimore, MDGerardo Heiss - Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, NCJohn A Heit - Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MNJae Hee Kang - Harvard Medical School, Boston, MASteven J Kittner - Department of Neurology, University of Maryland School of Medicine and Baltimore Veterans Affairs Medical Center, Baltimore, MDPeter Kraft - Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, MAWilliam Lowe - Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, ILMary L Marazita - Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh; Clinical and Translational Science Institute and Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PAKristine R Monroe - Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CALouis R Pasquale - Harvard Medical School, Boston, MAErin M Ramos - Office of Population Genomics, National Human Genome Research Institute, National Institutes of Health, Bethesda, MDRob M van Dam - Department of Epidemiology and Public Health and Medicine, Faculty of Medicine, National University of Singapore, Singapore; Department of Nutrition, Harvard School of Public Health, Boston, MAJenna Udren - Collaborative Health Studies Coordinating Center, Department of Biostatistics, University of Washington, Seattle, WAKayleen Williams - Collaborative Health Studies Coordinating Center, Department of Biostatistics, University of Washington, Seattle, WAGENEVA Consortium
- Contributors
- Jeffrey C Murray (Contributor) - University of Iowa, Dental Research
- Resource Type
- Journal article
- Publication Details
- Genetic epidemiology, Vol.35(3), pp.159-173
- DOI
- 10.1002/gepi.20564
- PMID
- 21284036
- PMCID
- PMC3055921
- NLM abbreviation
- Genet Epidemiol
- ISSN
- 0741-0395
- eISSN
- 1098-2272
- Language
- English
- Date published
- 04/2011
- Academic Unit
- Anatomy and Cell Biology; Stead Family Department of Pediatrics; Epidemiology; Pediatric Dentistry; Craniofacial Anomalies Research Center; Dental Research
- Record Identifier
- 9984025453602771
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