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Sung YJ, Wang L, Rankinen T, et al. Performance of genotype imputations using data from the 1000 Genomes Project. Hum Hered. 2011;73(1):18-25doi: 10.1159/000334084.
Sung, Y. J., Wang, L., Rankinen, T., Bouchard, C., & Rao, D. C. (2012). Performance of genotype imputations using data from the 1000 Genomes Project. Human heredity, 73(1), 18-25. https://doi.org/10.1159/000334084
Sung, Yun Ju, et al. "Performance of genotype imputations using data from the 1000 Genomes Project." Human heredity vol. 73,1 (2012): 18-25. doi: https://doi.org/10.1159/000334084
Sung YJ, Wang L, Rankinen T, Bouchard C, Rao DC. Performance of genotype imputations using data from the 1000 Genomes Project. Hum Hered. 2012;73(1):18-25. doi: 10.1159/000334084. Epub 2011 Dec 30. PMID: 22212296; PMCID: PMC3322630.
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Hum Hered. 2012;73(1):18-25. doi: 10.1159/000334084. Epub 2011 Dec 30.

Performance of genotype imputations using data from the 1000 Genomes Project.

Human heredity

Yun Ju Sung, Lihua Wang, Tuomo Rankinen, Claude Bouchard, D C Rao

Affiliations

  1. Division of Biostatistics, School of Medicine, Washington University in St. Louis, Mo. 63110, USA. [email protected]

PMID: 22212296 PMCID: PMC3322630 DOI: 10.1159/000334084

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.

Copyright © 2011 S. Karger AG, Basel.

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