ArticleStatistics and its interface2011
Practical Consideration of Genotype Imputation: Sample Size, Window Size, Reference Choice, and Untyped Rate.
Article in Statistics and its interface, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The trial behind it
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.
- Methods for multiancestry genome-wide association study meta-analysis.Annals of human genetics · 2025Review
- The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population.Bioinformatics (Oxford, England) · 2024Article
- A Pipeline for Phasing and Genotype Imputation on Mixed Human Data (Parents-Offspring Trios and Unrelated Subjects) by Reviewing Current Methods and Software.Life (Basel, Switzerland) · 2022Review
- Genotype imputation in case-only studies of gene-environment interaction: validity and power.Human genetics · 2021Article
- Accurate Imputation of Untyped Variants from Deep Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Genome-Wide Association Study of Metamizole-Induced Agranulocytosis in European Populations.Genes · 2020Article
- Association of PARP1-specific polymorphisms and haplotypes with non-small cell lung cancer subtypes.PloS one · 2020Article
- Rare Variants Imputation in Admixed Populations: Comparison Across Reference Panels and Bioinformatics Tools.Frontiers in genetics · 2019Article
- Genotype imputation performance of three reference panels using African ancestry individuals.Human genetics · 2018Article
- Influence of common and rare genetic variation on warfarin dose among African-Americans and European-Americans using the exome array.Pharmacogenomics · 2017Article
- Article
- GenomeLaser: fast and accurate haplotyping from pedigree genotypes.Bioinformatics (Oxford, England) · 2015Article
- References for Haplotype Imputation in the Big Data Era.Molecular biology (Los Angeles, Calif.) · 2015Article
- A hidden Markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns.Frontiers in genetics · 2014Article
- Genotype imputation accuracy with different reference panels in admixed populations.BMC proceedings · 2014Article
- MaCH-admix: genotype imputation for admixed populations.Genetic epidemiology · 2013Article
- Windfalls and pitfalls: Applications of population genetics to the search for disease genes.Evolution, medicine, and public health · 2013Article
- Reducing bias of allele frequency estimates by modeling SNP genotype data with informative missingness.Frontiers in genetics · 2012Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Imputation offers a promising way to infer the missing and/or untyped genotypes in genetic studies. In practice, however, many factors may affect the quality of imputation. In this study, we evaluated the influence of untyped rate, sizes of the study sample and the reference sample, window size, and reference choice (for admixed population), as the factors affecting the quality of imputation. The results show that in order to obtain good imputation quality, it is necessary to have an untyped rate less than 50%, a reference sample size greater than 50, and a window size of greater than 500 SNPs (roughly 1 MB in base pairs). Compared with the whole-region imputation, piecewise imputation with large-enough window sizes provides improved efficacy. For an admixed study sample, if only an external reference panel is used, it should include samples from the ancestral populations that represent the admixed population under investigation. Internal references are strongly recommended. When internal references are limited, however, augmentation by external references should be used carefully. More specifically, augmentation with samples from the major source populations of the admixture can lower the quality of imputation; augmentation with seemingly genetically unrelated cohorts may improve the quality of imputation.
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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.