A genotype imputation reference panel specific for native Southeast Asian populations.

Autor: Cengnata A; Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia., Deng L; State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.; Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China., Yap WS; Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia., Lim LR; Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia., Leong CO; Advanced Genomics Technology Center, AGTC Genomics Inc., Kuala Lumpur, Malaysia., Xu S; State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.; Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China.; Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.; School of Life Science and Technology, ShanghaiTech University, Shanghai, China., Hoh BP; Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, IMU University, Kuala Lumpur, Malaysia. hoh.boonpeng@gmail.com.
Jazyk: angličtina
Zdroj: NPJ genomic medicine [NPJ Genom Med] 2024 Oct 05; Vol. 9 (1), pp. 47. Date of Electronic Publication: 2024 Oct 05.
DOI: 10.1038/s41525-024-00435-7
Abstrakt: We report the development of a "Southeast Asian Specific (SEA-specific) Reference Panel" through a "Cross-panel Imputation" approach, consisting of 2550 samples derived from the GA100K, SG10K, and the Peninsular Malaysia Orang Asli (OA) datasets, covering 113,851,450 variants. The SEA-specific panel produced more high confidence variants than 1000 Genomes Project (1KGP) when imputing the OA (8.9 million SEA-specific vs 8.1 million 1KGP) and the Singapore Genome Variation Project (SGVP) (12.5 million SEA-specific vs 11.8 million 1KGP) genotyping datasets. Further, the SEA-specific panel imputed SNPs with better estimated quality scores (INFO, DR2 and R 2 ) on the OA genotyping dataset when comparing with TOPMED and the Human Genome Diversity Project, but performed similarly on SGVP dataset. This panel also exhibited higher recall and non-reference disconcordance rates, indicating the influence of ancestry closeness of the reference panel. However, we note that the imputation accuracy may be compromised by the size of the reference panel.
(© 2024. The Author(s).)
Databáze: MEDLINE
Externí odkaz: