ArticleNature communications2015
Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.
Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 229 papers, 13 of them syntheses that pooled it.
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Who cites it
229 citing papers in PubMed, 13 syntheses or guidelines pooled it.
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- Multiomic integration analysis identifies atherogenic metabolites mediating between novel immune genes and cardiovascular risk.Genome medicine · 2024Pooled it
- Meta-imputation: An efficient method to combine genotype data after imputation with multiple reference panels.American journal of human genetics · 2022Pooled it
- Endogenous DHEAS Is Causally Linked With Lumbar Spine Bone Mineral Density and Forearm Fractures in Women.The Journal of clinical endocrinology and metabolism · 2022Pooled it
- A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis.Communications biology · 2021Pooled it
- Population-specific and trans-ancestry genome-wide analyses identify distinct and shared genetic risk loci for coronary artery disease.Nature genetics · 2020Pooled it
- Genome-wide association study implicates immune dysfunction in the development of Hodgkin lymphoma.Blood · 2018Pooled it
- Multitrait genome association analysis identifies new susceptibility genes for human anthropometric variation in the GCAT cohort.Journal of medical genetics · 2018Pooled it
- Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma.Nature communications · 2018Pooled it
- Genome-wide meta-analyses of stratified depression in Generation Scotland and UK Biobank.Translational psychiatry · 2018Pooled it
- Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility.Nature communications · 2017Pooled it
- Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis.American journal of human genetics · 2017Pooled it
- Genetically determined very low lipoprotein(a) is not associated with type 2 diabetes and glycemic traits.American journal of preventive cardiology · 2027Article
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- Deep learning aging marker from retinal images unveils sex-specific clinical and genetic signatures.Nature communications · 2026Article
- Associations of polygenic risk scores for type 2 diabetes with metabolic measures in Pacific Islanders from Guam and Saipan.Journal of human genetics · 2026Article
- The genetics of fibromyalgia and its relationships to psychiatric and medical traits.Nature communications · 2026Article
- VN1K is a pangenome-informed multi-omics and phenomics resource for the Vietnamese population.Nature communications · 2026Article
169 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
Abstract
Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population. We show that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling. We also present a method for combining WGS panels to improve variant coverage and downstream imputation accuracy, which we illustrate by integrating 7,562 WGS haplotypes from the UK10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing imputation accuracy for rare variants.
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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 OpenQuestion graph.