Mitt, Mario, Kals, Mart, Parn, Kalle, Gabriel, Stacey B, Lander, Eric S, Palotie, Aarno, Ripatti, Samuli, Morris, Andrew P, Metspalu, Andres, Esko, Tonu et al (show 2 more authors)
(2016)
Improved Imputation Accuracy of Rare and Low-Frequency Genetic Variants Using Population-Specific High-Coverage Whole-Genome Sequencing Data Based Imputation Reference Panel.
HUMAN HEREDITY, 81 (4).
p. 235.
Abstract
Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 ×) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0.25% of adult Estonians). Although the Estonian-specific panel contains fewer haplotypes and variants, the imputation confidence and accuracy of imputed low-frequency and rare variants was significantly higher. The results indicate the utility of population-specific reference panels for human genetic studies.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Humans, Sequence Analysis, DNA, Gene Frequency, Haplotypes, Polymorphism, Single Nucleotide, Genome, Human, Reference Standards, Female, Male, Genome-Wide Association Study |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 28 Apr 2017 14:07 |
| Last Modified: | 19 Jan 2023 07:05 |
| DOI: | 10.1038/ejhg.2017.51 |
| Open Access URL: | http://www.nature.com.edgesuite.net/ejhg/journal/v... |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3007176 |
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