ArticlePLoS genetics2020
Genotype imputation using the Positional Burrows Wheeler Transform.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers, 4 of them syntheses that pooled it.
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Who cites it
146 citing papers in PubMed, 4 syntheses or guidelines pooled it, 228 citations in OpenAlex.
- Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.Nature communications · 2025Pooled it
- Genome-wide meta-analysis identifies ancestry-specific loci for Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Pooled it
- A systematic review of analytical methods used in genetic association analysis of the X-chromosome.Briefings in bioinformatics · 2022Pooled it
- Data Integration, Imputation, and Meta-analysis for Genome-Wide Association Studies.Methods in molecular biology (Clifton, N.J.) · 2022Pooled it
- A Run-Length-Compressed Skiplist Data Structure for Dynamic GBWTs Supports Time- and Space-Efficient Pangenome Operations over Syncmers.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- GPC: An expressive and tractable deep generative model for genetic variation data.PLoS genetics · 2026Article
- Accurate imputation of inversions in human genomes using different algorithms and data sources.NAR genomics and bioinformatics · 2026Article
- Parental haplotype reconstruction in up to 440,209 UK and Estonian individuals reveals recent assortative mating dynamics.Nature human behaviour · 2026Article
- Functional genomic dissection and prediction of body size traits in pigs.Genetics, selection, evolution : GSE · 2026Article
- IBAS: Interaction-bridged association studies discovering novel genes underlying complex traits.PLoS computational biology · 2026Article
- Local Enrichment of Multi-SNP Markers Improves Genomic Prediction from Low-Density Genotyping in Pacific White Shrimp.International journal of molecular sciences · 2026Article
- Popformer: Learning general signatures of positive selection with a self-supervised transformer.PLoS computational biology · 2026Article
- RLBWT-based LCP computation in compressed space for terabase-scale pangenome analysis.Bioinformatics (Oxford, England) · 2026Article
- A scalable framework for single-cell eQTL mapping uncovers genetic regulators of meat production traits in pigs.Journal of animal science and biotechnology · 2026Article
- Selphi, a tool for improving genotype imputation accuracy.Scientific reports · 2026Article
- Unravelling the genetic architecture of cerebral small vessel disease in the context of stroke.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2026Review
- Identifying Single-Cell Expression Quantitative Trait Loci Using a Bootstrap Penalized Hurdle Model.Genes · 2026Article
- GS-Impute: A neural network framework for accurate imputation of low-density markers in across-population genomic selection.Plant communications · 2026Article
- Highly efficient genotype compression leveraging genealogical relatedness.bioRxiv : the preprint server for biology · 2026Article
- A rapid review of genetic association studies of parent-of-origin effects and fetal growth.Molecular and cellular pediatrics · 2026Review
86 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Genotype imputation is the process of predicting unobserved genotypes in a sample of individuals using a reference panel of haplotypes. In the last 10 years reference panels have increased in size by more than 100 fold. Increasing reference panel size improves accuracy of markers with low minor allele frequencies but poses ever increasing computational challenges for imputation methods. Here we present IMPUTE5, a genotype imputation method that can scale to reference panels with millions of samples. This method continues to refine the observation made in the IMPUTE2 method, that accuracy is optimized via use of a custom subset of haplotypes when imputing each individual. It achieves fast, accurate, and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT). By using the PBWT data structure at genotyped markers, IMPUTE5 identifies locally best matching haplotypes and long identical by state segments. The method then uses the selected haplotypes as conditioning states within the IMPUTE model. Using the HRC reference panel, which has ∼65,000 haplotypes, we show that IMPUTE5 is up to 30x faster than MINIMAC4 and up to 3x faster than BEAGLE5.1, and uses less memory than both these methods. Using simulated reference panels we show that IMPUTE5 scales sub-linearly with reference panel size. For example, keeping the number of imputed markers constant, increasing the reference panel size from 10,000 to 1 million haplotypes requires less than twice the computation time. As the reference panel increases in size IMPUTE5 is able to utilize a smaller number of reference haplotypes, thus reducing computational cost.
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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.