ArticleHuman heredity2012
Performance of genotype imputations using data from the 1000 Genomes Project.
Article in Human heredity, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 2 of them syntheses that pooled it.
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Who cites it
28 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as candidates for hearing function and loss.Human molecular genetics · 2015Pooled it
- Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.Nature genetics · 2014Pooled it
- Insights into X-Linked Susceptibility to Parkinson's Disease in the South African Population.medRxiv : the preprint server for health sciences · 2025Article
- The phenotypic and genetic association between endometriosis and immunological diseases.Human reproduction (Oxford, England) · 2025Article
- A joint use of pooling and imputation for genotyping SNPs.BMC bioinformatics · 2022Article
- Migraine-Associated Common Genetic Variants Confer Greater Risk of Posterior vs. Anterior Circulation Ischemic Stroke☆.Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association · 2022Article
- A Multiancestry Sex-Stratified Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus.The Journal of infectious diseases · 2021Article
- The analysis of APOL1 genetic variation and haplotype diversity provided by 1000 Genomes project.BMC nephrology · 2017Article
- Resequencing Study Identifies Rare Renin-Angiotensin-Aldosterone System Variants Associated With Blood Pressure Salt-Sensitivity: The GenSalt Study.American journal of hypertension · 2017Article
- Article
- PreCimp: Pre-collapsing imputation approach increases imputation accuracy of rare variants in terms of collapsed variables.Genetic epidemiology · 2017Article
- A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples.Scientific reports · 2016Article
- Genomic and transcriptomic predictors of triglyceride response to regular exercise.British journal of sports medicine · 2015Article
- Improving accuracy of rare variant imputation with a two-step imputation approach.European journal of human genetics : EJHG · 2015Article
- Performance of genotype imputation for low frequency and rare variants from the 1000 genomes.PloS one · 2015Article
- Imputation of the rare HOXB13 G84E mutation and cancer risk in a large population-based cohort.PLoS genetics · 2015Article
- Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle.Genetics, selection, evolution : GSE · 2014Article
- Jumping on the Train of Personalized Medicine: A Primer for Non-Geneticist Clinicians: Part 1. Fundamental Concepts in Molecular Genetics.Current psychiatry reviews · 2014Article
- Lupus risk variants in the PXK locus alter B-cell receptor internalization.Frontiers in genetics · 2014Article
- The future for genetic studies in reproduction.Molecular human reproduction · 2014Review
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5 authors.
Funding
Abstract
Genotype imputations based on 1000 Genomes (1KG) Project data have the advantage of imputing many more SNPs than imputations based on HapMap data. It also provides an opportunity to discover associations with relatively rare variants. Recent investigations are increasingly using 1KG data for genotype imputations, but only limited evaluations of the performance of this approach are available. In this paper, we empirically evaluated imputation performance using 1KG data by comparing imputation results to those using the HapMap Phase II data that have been widely used. We used three reference panels: the CEU panel consisting of 120 haplotypes from HapMap II and 1KG data (June 2010 release) and the EUR panel consisting of 566 haplotypes also from 1KG data (August 2010 release). We used Illumina 324,607 autosomal SNPs genotyped in 501 individuals of European ancestry. Our most important finding was that both 1KG reference panels provided much higher imputation yield than the HapMap II panel. There were more than twice as many successfully imputed SNPs as there were using the HapMap II panel (6.7 million vs. 2.5 million). Our second most important finding was that accuracy using both 1KG panels was high and almost identical to accuracy using the HapMap II panel. Furthermore, after removing SNPs with MACH Rsq <0.3, accuracy for both rare and low frequency SNPs was very high and almost identical to accuracy for common SNPs. We found that imputation using the 1KG-EUR panel had advantages in successfully imputing rare, low frequency and common variants. Our findings suggest that 1KG-based imputation can increase the opportunity to discover significant associations for SNPs across the allele frequency spectrum. Because the 1KG Project is still underway, we expect that later versions will provide even better imputation performance.
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