Evaluation of imputation performance of multiple reference panels in a Pakistani population
Summary: 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 ance...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-04-01
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| Series: | HGG Advances |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666247724001350 |
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| author | Jiayi Xu Dongjing Liu Arsalan Hassan Giulio Genovese Alanna C. Cote Brian Fennessy Esther Cheng Alexander W. Charney James A. Knowles Muhammad Ayub Roseann E. Peterson Tim B. Bigdeli Laura M. Huckins |
| author_facet | Jiayi Xu Dongjing Liu Arsalan Hassan Giulio Genovese Alanna C. Cote Brian Fennessy Esther Cheng Alexander W. Charney James A. Knowles Muhammad Ayub Roseann E. Peterson Tim B. Bigdeli Laura M. Huckins |
| author_sort | Jiayi Xu |
| collection | DOAJ |
| description | Summary: 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. |
| format | Article |
| id | doaj-art-64265c7a04a44c38a3f1cf2e0e2b716a |
| institution | Kabale University |
| issn | 2666-2477 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | HGG Advances |
| spelling | doaj-art-64265c7a04a44c38a3f1cf2e0e2b716a2025-01-08T04:53:42ZengElsevierHGG Advances2666-24772025-04-0162100395Evaluation of imputation performance of multiple reference panels in a Pakistani populationJiayi Xu0Dongjing Liu1Arsalan Hassan2Giulio Genovese3Alanna C. Cote4Brian Fennessy5Esther Cheng6Alexander W. Charney7James A. Knowles8Muhammad Ayub9Roseann E. Peterson10Tim B. Bigdeli11Laura M. Huckins12Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA; Corresponding authorIcahn School of Medicine at Mount Sinai, New York, NY 10029, USAUniversity of Peshawar, Khyber Pakhtunkhwa, Peshawar 25120, Pakistan; Institute of Omics and Health Research, Lahore, PakistanProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USAIcahn School of Medicine at Mount Sinai, New York, NY 10029, USAIcahn School of Medicine at Mount Sinai, New York, NY 10029, USAIcahn School of Medicine at Mount Sinai, New York, NY 10029, USAIcahn School of Medicine at Mount Sinai, New York, NY 10029, USAThe Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USAUniversity College London, London WC1E 6BT, UKDepartment of Psychiatry and Behavioral Sciences, Institute for Genomics in Health, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USADepartment of Psychiatry and Behavioral Sciences, Institute for Genomics in Health, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USADepartment of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2666247724001350Geneticsgenome-wide association studiesimputationimputation panelsSouth Asian ancestryPakistan |
| spellingShingle | Jiayi Xu Dongjing Liu Arsalan Hassan Giulio Genovese Alanna C. Cote Brian Fennessy Esther Cheng Alexander W. Charney James A. Knowles Muhammad Ayub Roseann E. Peterson Tim B. Bigdeli Laura M. Huckins Evaluation of imputation performance of multiple reference panels in a Pakistani population HGG Advances Genetics genome-wide association studies imputation imputation panels South Asian ancestry Pakistan |
| title | Evaluation of imputation performance of multiple reference panels in a Pakistani population |
| title_full | Evaluation of imputation performance of multiple reference panels in a Pakistani population |
| title_fullStr | Evaluation of imputation performance of multiple reference panels in a Pakistani population |
| title_full_unstemmed | Evaluation of imputation performance of multiple reference panels in a Pakistani population |
| title_short | Evaluation of imputation performance of multiple reference panels in a Pakistani population |
| title_sort | evaluation of imputation performance of multiple reference panels in a pakistani population |
| topic | Genetics genome-wide association studies imputation imputation panels South Asian ancestry Pakistan |
| url | http://www.sciencedirect.com/science/article/pii/S2666247724001350 |
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