ArticleGenetic epidemiology2017
Improving power of association tests using multiple sets of imputed genotypes from distributed reference panels.
Article in Genetic epidemiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis 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
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-imputation: An efficient method to combine genotype data after imputation with multiple reference panels.American journal of human genetics · 2022Pooled it
- Ancestral diversity in complex disease genetics: from discovery to translation.Nature reviews. Genetics · 2026Review
- Genotype imputation from low-coverage WGS using haplotype reference panels in cultivated strawberry.BMC genomics · 2025Article
- How local reference panels improve imputation in French populations.Scientific reports · 2024Article
- Construction of a strawberry breeding core collection to capture and exploit genetic variation.BMC genomics · 2023Article
- Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels.Briefings in bioinformatics · 2023Article
- Sex-Specific Survival Bias and Interaction Modeling in Coronary Artery Disease Risk Prediction.Circulation. Genomic and precision medicine · 2023Article
- The HUNT study: A population-based cohort for genetic research.Cell genomics · 2022Article
- An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population.Science China. Life sciences · 2022Article
- Taller height and risk of coronary heart disease and cancer: A within-sibship Mendelian randomization study.eLife · 2022Article
- Best practices for analyzing imputed genotypes from low-pass sequencing in dogs.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Article
- On the application, reporting, and sharing of in silico simulations for genetic studies.Genetic epidemiology · 2021Review
- MEPE loss-of-function variant associates with decreased bone mineral density and increased fracture risk.Nature communications · 2020Article
- Sequencing and imputation in GWAS: Cost-effective strategies to increase power and genomic coverage across diverse populations.Genetic epidemiology · 2020Article
- Kinpute: using identity by descent to improve genotype imputation.Bioinformatics (Oxford, England) · 2019Article
- Genotype imputation for Han Chinese population using Haplotype Reference Consortium as reference.Human genetics · 2018Article
- Serum 25-hydroxyvitamin D levels and risk of lung cancer and histologic types: a Mendelian randomisation analysis of the HUNT study.The European respiratory journal · 2018Article
- Electronic health records: the next wave of complex disease genetics.Human molecular genetics · 2018Review
Corrections and comments
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Authors and funding
13 authors.
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Abstract
The accuracy of genotype imputation depends upon two factors: the sample size of the reference panel and the genetic similarity between the reference panel and the target samples. When multiple reference panels are not consented to combine together, it is unclear how to combine the imputation results to optimize the power of genetic association studies. We compared the accuracy of 9,265 Norwegian genomes imputed from three reference panels-1000 Genomes phase 3 (1000G), Haplotype Reference Consortium (HRC), and a reference panel containing 2,201 Norwegian participants from the population-based Nord Trøndelag Health Study (HUNT) from low-pass genome sequencing. We observed that the population-matched reference panel allowed for imputation of more population-specific variants with lower frequency (minor allele frequency (MAF) between 0.05% and 0.5%). The overall imputation accuracy from the population-specific panel was substantially higher than 1000G and was comparable with HRC, despite HRC being 15-fold larger. These results recapitulate the value of population-specific reference panels for genotype imputation. We also evaluated different strategies to utilize multiple sets of imputed genotypes to increase the power of association studies. We observed that testing association for all variants imputed from any panel results in higher power to detect association than the alternative strategy of including only one version of each genetic variant, selected for having the highest imputation quality metric. This was particularly true for lower frequency variants (MAF < 1%), even after adjusting for the additional multiple testing burden.
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