ArticleAmerican journal of human genetics2009
Genotype-imputation accuracy across worldwide human populations.
Article in American journal of human genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers, 13 of them syntheses that pooled it.
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Who cites it
172 citing papers in PubMed, 13 syntheses or guidelines pooled it.
- Validation of Polygenic Scores for QT Interval in Clinical Populations.Circulation. Cardiovascular genetics · 2017Pooled it
- Lipids, lipid genes, and incident age-related macular degeneration: the three continent age-related macular degeneration consortium.American journal of ophthalmology · 2014Pooled it
- Imputation-based meta-analysis of severe malaria in three African populations.PLoS genetics · 2013Pooled it
- Genetic analysis of a population heavy drinking phenotype identifies risk variants in whites.Journal of clinical psychopharmacology · 2013Pooled it
- Common variants at 11p13 are associated with susceptibility to tuberculosis.Nature genetics · 2012Pooled it
- Genetic association for renal traits among participants of African ancestry reveals new loci for renal function.PLoS genetics · 2011Pooled it
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- Genome-wide association analysis and fine mapping of NT-proBNP level provide novel insight into the role of the MTHFR-CLCN6-NPPA-NPPB gene cluster.Human molecular genetics · 2011Pooled it
- Meta-analysis of genome-wide association data of bipolar disorder and major depressive disorder.Molecular psychiatry · 2011Pooled it
- Meta-analysis of genome-wide association data identifies a risk locus for major mood disorders on 3p21.1.Nature genetics · 2010Pooled it
- Collaborative meta-analysis: associations of 150 candidate genes with osteoporosis and osteoporotic fracture.Annals of internal medicine · 2009Pooled it
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- Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.PLoS genetics · 2009Pooled it
- Twins, tissue, and time: an assessment of SNPs and CNVs.Twin research and human genetics : the official journal of the International Society for Twin Studies · 2012Trial
- A population-specific genomic reference panel for Taiwan: NHRI-RP-1.Journal of biomedical science · 2026Article
- A Pseudohaploid-Based Imputation Strategy for Interspecific FMolecular ecology · 2026Article
- Reflections on the Human Genome Diversity Project: a conversation with Marcus W. Feldman, Henry T. Greely, and Mary-Claire King.Genetics · 2026Article
- High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.Genomics, proteomics & bioinformatics · 2025Review
- Methodological opportunities in genomic data analysis to advance health equity.Nature reviews. Genetics · 2025Review
- Characterization of the complex TB pharmacogenomic landscape in Africa using bioinformatic tools.Briefings in bioinformatics · 2025Article
112 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
A current approach to mapping complex-disease-susceptibility loci in genome-wide association (GWA) studies involves leveraging the information in a reference database of dense genotype data. By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed and tested for disease association. This imputation strategy has been successful for GWA studies in populations well represented by existing reference panels. We used genotypes at 513,008 autosomal single-nucleotide polymorphism (SNP) loci in 443 unrelated individuals from 29 worldwide populations to evaluate the "portability" of the HapMap reference panels for imputation in studies of diverse populations. When a single HapMap panel was leveraged for imputation of randomly masked genotypes, European populations had the highest imputation accuracy, followed by populations from East Asia, Central and South Asia, the Americas, Oceania, the Middle East, and Africa. For each population, we identified "optimal" mixtures of reference panels that maximized imputation accuracy, and we found that in most populations, mixtures including individuals from at least two HapMap panels produced the highest imputation accuracy. From a separate survey of additional SNPs typed in the same samples, we evaluated imputation accuracy in the scenario in which all genotypes at a given SNP position were unobserved and were imputed on the basis of data from a commercial "SNP chip," again finding that most populations benefited from the use of combinations of two or more HapMap reference panels. Our results can serve as a guide for selecting appropriate reference panels for imputation-based GWA analysis in diverse populations.
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