Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel
- Mitt, Mario
- Kals, Mart
- Pärn, Kalle
- Ripatti, Samuli
- Morris, Andrew P
- Metspalu, Andres
- Esko, Tõnu
- Mägi, Reedik
- Palta, Priit
- Gabriel, Stacey
- Lander, Eric Steven
- Palotie, Aarno
DOIAbstract
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 ...
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