ArticleNature genetics2023
Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 173 papers, 2 of them syntheses that pooled it.
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Who cites it
173 citing papers in PubMed, 2 syntheses or guidelines pooled it.
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- Disparities in ABO blood type determination across diverse ancestries: a systematic review and validation in the All of Us Research Program.Journal of the American Medical Informatics Association : JAMIA · 2024Pooled it
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- Quantifying the Evolutionary Potential for Delta Smelt Persistence in a Warming Habitat.Evolutionary applications · 2026Article
- Accurate imputation of inversions in human genomes using different algorithms and data sources.NAR genomics and bioinformatics · 2026Article
- Deviations from genetic additivity driven by rare variants at biobank scale.Nature communications · 2026Article
- Extending genome-wide association studies to admixed cohorts with high degrees of relatedness.Nature genetics · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Atlas of glomerular disease-specific genetic effects on blood transcriptome.medRxiv : the preprint server for health sciences · 2026Article
- Local Enrichment of Multi-SNP Markers Improves Genomic Prediction from Low-Density Genotyping in Pacific White Shrimp.International journal of molecular sciences · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Genome sequencing for the diagnosis of rare disorders: The Brazilian Rare Genomes Project.HGG advances · 2026Article
- Advancing risk gene discovery across the allele frequency spectrum.HGG advances · 2026Review
- Separating direct, indirect, and parent-of-origin genetic effects in the human population.Cell genomics · 2026Article
- A transparent and generalizable deep-learning framework for genomic ancestry prediction.American journal of human genetics · 2026Article
- Genetic and transcriptomic determinants of disseminated coccidioidomycosis identify a founder variant inmedRxiv : the preprint server for health sciences · 2026Article
- Direct probabilistic quantification of mosaic loss of chromosome Y from sequencing data.bioRxiv : the preprint server for biology · 2026Article
- DRIVE v3: Command Line Application for Identity-by-Descent Haplotype Clustering in Large Biobank Scale Data.Genetic epidemiology · 2026Article
- Ancient DNA evidence for the history of the Albanians.Nature human behaviour · 2026Article
113 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phasing involves distinguishing the two parentally inherited copies of each chromosome into haplotypes. Here, we introduce SHAPEIT5, a new phasing method that quickly and accurately processes large sequencing datasets and applied it to UK Biobank (UKB) whole-genome and whole-exome sequencing data. We demonstrate that SHAPEIT5 phases rare variants with low switch error rates of below 5% for variants present in just 1 sample out of 100,000. Furthermore, we outline a method for phasing singletons, which, although less precise, constitutes an important step towards future developments. We then demonstrate that the use of UKB as a reference panel improves the accuracy of genotype imputation, which is even more pronounced when phased with SHAPEIT5 compared with other methods. Finally, we screen the UKB data for loss-of-function compound heterozygous events and identify 549 genes where both gene copies are knocked out. These genes complement current knowledge of gene essentiality in the human genome.
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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 Socratic graph.