ArticleScientific reports2016
A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
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Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
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- Genome-wide Association Studies of over 30,000 Samples with Bone Mineral Density at Multiple Skeletal Sites and Its Clinical Relevance.Genomics, proteomics & bioinformatics · 2025Article
- A multi-trait genome-wide association study of coronary artery disease and subclinical atherosclerosis traits.Research square · 2025Article
- Relationship between inherited genetic variation and survival from colorectal cancer stratified by tumour location.Scientific reports · 2025Article
- SEAD reference panel with 22,134 haplotypes boosts rare variant imputation and genome-wide association analysis in Asian populations.Nature communications · 2024Article
- Identification of Causal Genes and Potential Drug Targets for Restless Legs Syndrome: A Comprehensive Mendelian Randomization Study.Pharmaceuticals (Basel, Switzerland) · 2024Article
- Association of polygenic liabilities for schizophrenia and bipolar disorder with educational attainment and cognitive aging.Translational psychiatry · 2024Article
- Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.bioRxiv : the preprint server for biology · 2024Article
- Genetic similarity between relatives provides evidence on the presence and history of assortative mating.Nature communications · 2024Article
- A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome.NPJ genomic medicine · 2024Article
- How local reference panels improve imputation in French populations.Scientific reports · 2024Article
- Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy.Frontiers in genetics · 2024Article
- A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population.Scientific reports · 2023Article
- Polygenic Susceptibility to Hypertension and Blood Pressure Control in Stroke Survivors.Neurology · 2023Article
- Article
- Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.Genetics, selection, evolution : GSE · 2022Article
- Article
- Emerging roles of rare and low-frequency genetic variants in type 1 diabetes mellitus.Journal of medical genetics · 2021Review
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Authors and funding
10 authors at 6 institutions in 4 countries.
Funding
Abstract
Imputation using the 1000 Genomes haplotype reference panel has been widely adapted to estimate genotypes in genome wide association studies. To evaluate imputation quality with a relatively larger reference panel and a reference panel composed of different ethnic populations, we conducted imputations in the Framingham Heart Study and the North Chinese Study using a combined reference panel from the 1000 Genomes (N = 1,092) and UK10K (N = 3,781) projects. For rare variants with 0.01% < MAF ≤ 0.5%, imputation in the Framingham Heart Study with the combined reference panel increased well-imputed genotypes (with imputation quality score ≥0.4) from 62.9% to 76.1% when compared to imputation with the 1000 Genomes. For the North Chinese samples, imputation of rare variants with 0.01% < MAF ≤ 0.5% with the combined reference panel increased well-imputed genotypes by from 49.8% to 61.8%. The predominant European ancestry of the UK10K and the combined reference panels may explain why there was less of an increase in imputation success in the North Chinese samples. Our results underscore the importance and potential of larger reference panels to impute rare variants, while recognizing that increasing ethnic specific variants in reference panels may result in better imputation for genotypes in some ethnic groups.
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