ArticlePloS one2010
Analyses and comparison of imputation-based association methods.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 2 syntheses or guidelines pooled it, 35 citations in OpenAlex.
- Meta-analysis of genome-wide association data identifies novel susceptibility loci for obesity.Human molecular genetics · 2014Pooled it
- Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.Nature genetics · 2013Pooled it
- Aggregating single nucleotide polymorphisms improves filtering for false-positive associations postimputation.G3 (Bethesda, Md.) · 2025Article
- The trans-ancestral genomic architecture of glycemic traits.Nature genetics · 2021Article
- Genome-wide association study of circulating interleukin 6 levels identifies novel loci.Human molecular genetics · 2021Article
- Genome-wide landscape establishes novel association signals for metabolic traits in the Arab population.Human genetics · 2021Article
- Assessment of Imputation Quality: Comparison of Phasing and Imputation Algorithms in Real Data.Frontiers in genetics · 2021Article
- Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population.Frontiers in genetics · 2019Article
- Rare Variants Imputation in Admixed Populations: Comparison Across Reference Panels and Bioinformatics Tools.Frontiers in genetics · 2019Article
- Association analysis of exome variants and refraction, axial length, and corneal curvature in a European-American population.Human mutation · 2018Article
- Influence of common and rare genetic variation on warfarin dose among African-Americans and European-Americans using the exome array.Pharmacogenomics · 2017Article
- Genetic variants in CETP increase risk of intracerebral hemorrhage.Annals of neurology · 2016Article
- An integrative imputation method based on multi-omics datasets.BMC bioinformatics · 2016Article
- A guide to genome-wide association analysis and post-analytic interrogation.Statistics in medicine · 2015Article
- Association studies with imputed variants using expectation-maximization likelihood-ratio tests.PloS one · 2014Article
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- Article
- Formin homology 2 domain containing 3 variants associated with hypertrophic cardiomyopathy.Circulation. Cardiovascular genetics · 2013Article
- 1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data.European journal of human genetics : EJHG · 2012Article
- Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs.BMC medical genomics · 2012Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Genotype imputation methods have become increasingly popular for recovering untyped genotype data. An important application with imputed genotypes is to test genetic association for diseases. Imputation-based association test can provide additional insight beyond what is provided by testing on typed tagging SNPs only. A variety of effective imputation-based association tests have been proposed. However, their performances are affected by a variety of genetic factors, which have not been well studied. In this study, using both simulated and real data sets, we investigated the effects of LD, MAF of untyped causal SNP and imputation accuracy rate on the performances of seven popular imputation-based association methods, including MACH2qtl/dat, SNPTEST, ProbABEL, Beagle, Plink, BIMBAM and SNPMStat. We also aimed to provide a comprehensive comparison among methods. Results show that: 1). imputation-based association tests can boost signals and improve power under medium and high LD levels, with the power improvement increasing with strengthening LD level; 2) the power increases with higher MAF of untyped causal SNPs under medium to high LD level; 3). under low LD level, a high imputation accuracy rate cannot guarantee an improvement of power; 4). among methods, MACH2qtl/dat, ProbABEL and SNPTEST perform similarly and they consistently outperform other methods. Our results are helpful in guiding the choice of imputation-based association test in practical application.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.