Evaluation of imputation performance of multiple reference panels in a Pakistani population
Genotype imputation is crucial for genome-wide association studies (GWASs), but reference panels and existing benchmarking studies prioritize European individuals. Consequently, it is unclear which publicly available reference panel should be used for Pakistani individuals, and whether ancestry composition or sample size of the panel matters more for imputation accuracy. Our study compared different reference panels to impute genotype data in 1,814 Pakistani individuals, finding the best performance balancing accuracy and coverage with meta-imputation with TOPMed and the expanded 1000 Genomes (ex1KG) reference. Imputation accuracy of ex1KG outperformed TOPMed for common variants despite its 30-fold smaller sample size, supporting efforts to create future panels with diverse populations.
Authors
- Arsalan Hassan (ORCID: https://orcid.org/0000-0002-3262-0277)
- Tim B. Bigdeli (ORCID: https://orcid.org/0000-0003-2215-5946)
- Laura M. Huckins (ORCID: https://orcid.org/0000-0002-5369-6502)
- Giulio Genovese (ORCID: https://orcid.org/0000-0003-3066-5575)
- Roseann E. Peterson (ORCID: https://orcid.org/0000-0001-6402-849X)
- Esther Cheng (ORCID: https://orcid.org/0000-0001-7383-2447)
- Alanna C. Cote (ORCID: https://orcid.org/0000-0001-7743-7815)
- Dongjing Liu (ORCID: https://orcid.org/0000-0002-9520-7789)
- Muhammad Ayub (ORCID: https://orcid.org/0000-0002-7111-1571)
- Brian Fennessy (ORCID: https://orcid.org/0000-0002-6222-6190)
- Jiayi Xu (ORCID: https://orcid.org/0000-0001-6379-386X)
- Alexander W. Charney (ORCID: https://orcid.org/0000-0001-8135-6858)
- James A. Knowles
Institutions
- Rutgers, The State University of New Jersey (US)
- Broad Institute (US)
- SUNY Downstate Health Sciences University (US)
- The University of Agriculture, Peshawar (PK)
- Yale University (US)
- University of Peshawar (PK)
- Environmental and Occupational Health Sciences Institute (US)
- Institute of Management Sciences Peshawar (PK)
- University College London (GB)
- Icahn School of Medicine at Mount Sinai (US)
Publication Details
- Journal
- Human Genetics and Genomics Advances
- Published
- 2024-12-18
- DOI
- https://doi.org/10.1016/j.xhgg.2024.100395
- Citations
- 3
- Primary Topic
- Body Composition Measurement Techniques
- Type
- article
- Field-Weighted Citation Impact
- 0.98
Funders
- Brain and Behavior Research Foundation
- University of Michigan
- National Alliance for Research on Schizophrenia and Depression
- National Institutes of Health
- National Institute of Mental Health
- National Institute of Environmental Health Sciences