Meta-analysis in genome-wide association datasets: strategies and application in Parkinson disease

• Published in: PloS one Vol. 2; no. 2; p. e196
• Main Authors: Evangelou, Evangelos, Maraganore, Demetrius M, Ioannidis, John P A
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 07-02-2007; Public Library of Science (PLoS)
• Subjects: Age; Chromosome 11; Chromosome 3; Chromosome 4; Chromosomes; Consortia; Data processing; Datasets; Diabetes; Disease susceptibility; Epidemiology; Genetic aspects; Genetic diversity; Genetic effects; Genetic Predisposition to Disease; Genetic variance; Genetics and Genomics/Complex Traits; Genetics and Genomics/Genetics of Disease; Genome-wide association studies; Genome-Wide Association Study - statistics & numerical data; Genomes; Genomics; Genotype; Genotyping; Handbooks; Heart attacks; Heterogeneity; Humans; Macular degeneration; Medical research; Medicine; Meta-analysis; Meta-Analysis as Topic; Movement disorders; Neurodegenerative diseases; Neurological Disorders/Movement Disorders; Nuclear electric power generation; Obesity; Odds Ratio; Parkinson disease; Parkinson Disease - epidemiology; Parkinson Disease - genetics; Parkinson's disease; Polymorphism; Polymorphism, Single Nucleotide; Prospective Studies; Public Health and Epidemiology/Epidemiology; Siblings; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Studies; Greece
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0000196

Genome-wide association studies hold substantial promise for identifying common genetic variants that regulate susceptibility to complex diseases. However, for the detection of small genetic effects, single studies may be underpowered. Power may be improved by combining genome-wide datasets with meta-analytic techniques.
Both single and two-stage genome-wide data may be combined and there are several possible strategies. In the two-stage framework, we considered the options of (1) enhancement of replication data and (2) enhancement of first-stage data, and then, we also considered (3) joint meta-analyses including all first-stage and second-stage data. These strategies were examined empirically using data from two genome-wide association studies (three datasets) on Parkinson disease. In the three strategies, we derived 12, 5, and 49 single nucleotide polymorphisms that show significant associations at conventional levels of statistical significance. None of these remained significant after conservative adjustment for the number of performed analyses in each strategy. However, some may warrant further consideration: 6 SNPs were identified with at least 2 of the 3 strategies and 3 SNPs [rs1000291 on chromosome 3, rs2241743 on chromosome 4 and rs3018626 on chromosome 11] were identified with all 3 strategies and had no or minimal between-dataset heterogeneity (I(2) = 0, 0 and 15%, respectively). Analyses were primarily limited by the suboptimal overlap of tested polymorphisms across different datasets (e.g., only 31,192 shared polymorphisms between the two tier 1 datasets).
Meta-analysis may be used to improve the power and examine the between-dataset heterogeneity of genome-wide association studies. Prospective designs may be most efficient, if they try to maximize the overlap of genotyping platforms and anticipate the combination of data across many genome-wide association studies.