ArticleGenetics2012
A coalescent model for genotype imputation.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- A pharmacokinetic/pharmacodynamic model of tumor lysis syndrome in chronic lymphocytic leukemia patients treated with flavopiridol.Clinical cancer research : an official journal of the American Association for Cancer Research · 2013Trial
- ALGI: Sparse Convolutional Denoising Autoencoder Utilizing Local Genomic Information for Genotype Imputation.Animals : an open access journal from MDPI · 2026Article
- Optimal Reference Panel Design in Ancient DNA Imputation from Coalescent Theory, Simulation, and Real Data Application with an Ancient Reference Panel.bioRxiv : the preprint server for biology · 2026Article
- MetaGLIMPSE: Meta-imputation of low-coverage sequencing data for modern and ancient genomes.American journal of human genetics · 2026Article
- MetaGLIMPSE: Meta Imputation of Low Coverage Sequencing Data for Modern and Ancient Genomes.bioRxiv : the preprint server for biology · 2025Article
- Tree-based QTL mapping with expected local genetic relatedness matrices.American journal of human genetics · 2023Article
- Tree-based QTL mapping with expected local genetic relatedness matrices.bioRxiv : the preprint server for biology · 2023Article
- Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples.Genetics · 2022Article
- Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms.Genetics · 2021Article
- The Opportunities and Challenges of Integrating Population Histories Into Genetic Studies for Diverse Populations: A Motivating Example From Native Hawaiians.Frontiers in genetics · 2021Article
- Population-specific reference panels are crucial for genetic analyses: an example of the CREBRF locus in Native Hawaiians.Human molecular genetics · 2020Article
- Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure.BMC genomics · 2017Article
- Latitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes.G3 (Bethesda, Md.) · 2016Article
- Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression.Genetic epidemiology · 2016Article
- Article
- References for Haplotype Imputation in the Big Data Era.Molecular biology (Los Angeles, Calif.) · 2015Article
- Choosing Subsamples for Sequencing Studies by Minimizing the Average Distance to the Closest Leaf.Genetics · 2015Article
- Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.Nature communications · 2015Article
- Imputation of the rare HOXB13 G84E mutation and cancer risk in a large population-based cohort.PLoS genetics · 2015Article
- Theory and applications of a deterministic approximation to the coalescent model.Theoretical population biology · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The potential for imputed genotypes to enhance an analysis of genetic data depends largely on the accuracy of imputation, which in turn depends on properties of the reference panel of template haplotypes used to perform the imputation. To provide a basis for exploring how properties of the reference panel affect imputation accuracy theoretically rather than with computationally intensive imputation experiments, we introduce a coalescent model that considers imputation accuracy in terms of population-genetic parameters. Our model allows us to investigate sampling designs in the frequently occurring scenario in which imputation targets and templates are sampled from different populations. In particular, we derive expressions for expected imputation accuracy as a function of reference panel size and divergence time between the reference and target populations. We find that a modestly sized "internal" reference panel from the same population as a target haplotype yields, on average, greater imputation accuracy than a larger "external" panel from a different population, even if the divergence time between the two populations is small. The improvement in accuracy for the internal panel increases with increasing divergence time between the target and reference populations. Thus, in humans, our model predicts that imputation accuracy can be improved by generating small population-specific custom reference panels to augment existing collections such as those of the HapMap or 1000 Genomes Projects. Our approach can be extended to understand additional factors that affect imputation accuracy in complex population-genetic settings, and the results can ultimately facilitate improvements in imputation study designs.
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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.