ArticleNature genetics2021
Rapid genotype imputation from sequence with reference panels.
Article in Nature genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
56 citing papers in PubMed.
- Low-Coverage Whole-Genome Resequencing in Livestock and Poultry: Statistical Foundations, Applications and Future Directions.Biology · 2026Review
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- MetaGLIMPSE: Meta-imputation of low-coverage sequencing data for modern and ancient genomes.American journal of human genetics · 2026Article
- Skim-sequencing for genomic selection in wheat: a comparison of marker platforms.The plant genome · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- The Neijiang pig T2T genome reveals domestication history and germplasm traits of Southwest Chinese local breeds.Communications biology · 2026Article
- A simple demonstration of a privacy-preserving de-centralised genotype imputation workflow.PloS one · 2026Article
- High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.Genomics, proteomics & bioinformatics · 2025Review
- Flexible read-aware genotype imputation from sequence using biobank sized reference panels.Nature communications · 2025Article
- Low-Coverage Whole-Genome Sequencing (lcWGS) in Cattle: Analysis of Potential and Prospects for Application.Animals : an open access journal from MDPI · 2025Review
- Pangenome-based genome inference using integer programming.Genome research · 2025Article
- A low-coverage skim-sequencing and imputation pipeline for genomic selection.The plant genome · 2025Article
- Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Genotype imputation from low-coverage data for medical and population genetic analyses.Genome research · 2025Article
- MetaGLIMPSE: Meta Imputation of Low Coverage Sequencing Data for Modern and Ancient Genomes.bioRxiv : the preprint server for biology · 2025Article
- Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins.Molecular biology and evolution · 2025Article
- GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes.Genomics, proteomics & bioinformatics · 2025Article
- Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden.Genome biology · 2025Article
- Whole genome and transcriptome analyses identify genetic markers associated with growth traits in Qinchuan black pig.BMC genomics · 2025Article
- DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Inexpensive genotyping methods are essential to modern genomics. Here we present QUILT, which performs diploid genotype imputation using low-coverage whole-genome sequence data. QUILT employs Gibbs sampling to partition reads into maternal and paternal sets, facilitating rapid haploid imputation using large reference panels. We show this partitioning to be accurate over many megabases, enabling highly accurate imputation close to theoretical limits and outperforming existing methods. Moreover, QUILT can impute accurately using diverse technologies, including long reads from Oxford Nanopore Technologies, and a new form of low-cost barcoded Illumina sequencing called haplotagging, with the latter showing improved accuracy at low coverages. Relative to DNA genotyping microarrays, QUILT offers improved accuracy at reduced cost, particularly for diverse populations that are traditionally underserved in modern genomic analyses, with accuracy nearly doubling at rare SNPs. Finally, QUILT can accurately impute (four-digit) human leukocyte antigen types, the first such method from low-coverage sequence data.
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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.