A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples

Wen Chi Chou; Hou Feng Zheng; Chia Ho Cheng; Han Yan; Li Wang; Fang Han; J. Brent Richards; David Karasik; Douglas P. Kiel; Yi Hsiang Hsu

doi:10.1038/srep39313

A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples

Wen Chi Chou, Hou Feng Zheng, Chia Ho Cheng, Han Yan, Li Wang, Fang Han, J. Brent Richards, David Karasik, Douglas P. Kiel, Yi Hsiang Hsu

Research output: Contribution to journal › Article › peer-review

22 Scopus citations

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.

Original language	English
Article number	39313
Journal	Scientific Reports
Volume	6
DOIs	https://doi.org/10.1038/srep39313
State	Published - 22 Dec 2016
Externally published	Yes

Bibliographical note

Publisher Copyright:
© The Author(s) 2016.

Funding

We thank L. Adrienne Cupples, Ching-Ti Liu, and Yanhua Zhou for helpful suggestions and comments. Our work was supported by the NHLBI in collaboration with Boston University (BU) (N01-HC-25195), and its contract with Affymetrix, Inc., for genome-wide genotyping services (N02-HL-6-4278), for quality control by FHS investigators using genotypes in the SNP Health Association Resource (SHARe) project. The Framingham Osteoporosis Study is supported by NIAMS (R01 AR/AG 41398, R01 AR 061162, and R01 AR 061445).

Funders	Funder number
National Heart, Lung, and Blood Institute	N02-HL-6-4278, N01-HC-25195
National Institute of Arthritis and Musculoskeletal and Skin Diseases	R01 AR 061162, R01 AR/AG 41398, R01AR061445
Filson Historical Society

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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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AU - Wang, Li

AU - Han, Fang

AU - Richards, J. Brent

AU - Karasik, David

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A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples

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