ArticleHuman molecular genetics2016
Improved imputation accuracy in Hispanic/Latino populations with larger and more diverse reference panels: applications in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).
Article in Human molecular genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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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
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-wide association study of cognitive function in diverse Hispanics/Latinos: results from the Hispanic Community Health Study/Study of Latinos.Translational psychiatry · 2020Pooled it
- Non-genetic component of height as a surrogate marker for childhood socioeconomic position and its association with cardiovascular and brain health: results from HCHS/SOL.medRxiv : the preprint server for health sciences · 2026Article
- SEAD reference panel with 22,134 haplotypes boosts rare variant imputation and genome-wide association analysis in Asian populations.Nature communications · 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
- 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
- Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa.Tropical animal health and production · 2022Article
- A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants.BMC bioinformatics · 2021Article
- Multiple-ancestry genome-wide association study identifies 27 loci associated with measures of hemolysis following blood storage.The Journal of clinical investigation · 2021Article
- Rare Variants Imputation in Admixed Populations: Comparison Across Reference Panels and Bioinformatics Tools.Frontiers in genetics · 2019Article
- Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population.Frontiers in genetics · 2019Article
- Genome-Wide Association Study of Heavy Smoking and Daily/Nondaily Smoking in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Imputation is commonly used in genome-wide association studies to expand the set of genetic variants available for analysis. Larger and more diverse reference panels, such as the final Phase 3 of the 1000 Genomes Project, hold promise for improving imputation accuracy in genetically diverse populations such as Hispanics/Latinos in the USA. Here, we sought to empirically evaluate imputation accuracy when imputing to a 1000 Genomes Phase 3 versus a Phase 1 reference, using participants from the Hispanic Community Health Study/Study of Latinos. Our assessments included calculating the correlation between imputed and observed allelic dosage in a subset of samples genotyped on a supplemental array. We observed that the Phase 3 reference yielded higher accuracy at rare variants, but that the two reference panels were comparable at common variants. At a sample level, the Phase 3 reference improved imputation accuracy in Hispanic/Latino samples from the Caribbean more than for Mainland samples, which we attribute primarily to the additional reference panel samples available in Phase 3. We conclude that a 1000 Genomes Project Phase 3 reference panel can yield improved imputation accuracy compared with Phase 1, particularly for rare variants and for samples of certain genetic ancestry compositions. Our findings can inform imputation design for other genome-wide association studies of participants with diverse ancestries, especially as larger and more diverse reference panels continue to become available.
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