一个专门针对东南亚本土人群的基因型填充参考面板。
A genotype imputation reference panel specific for native Southeast Asian populations.
作者信息
Cengnata Alvin, Deng Lian, Yap Wai-Sum, Lim Lay-Hong Renee, Leong Chee-Onn, Xu Shuhua, Hoh Boon-Peng
机构信息
Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia.
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.
出版信息
NPJ Genom Med. 2024 Oct 5;9(1):47. doi: 10.1038/s41525-024-00435-7.
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) 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.
我们报告了通过“跨面板推算”方法开发的“东南亚特异性（SEA特异性）参考面板”，该面板由来自GA100K、SG10K和马来西亚半岛原住民（OA）数据集的2550个样本组成，涵盖113,851,450个变异。在推算OA（890万个SEA特异性变异对810万个千人基因组计划（1KGP）变异）和新加坡基因组变异项目（SGVP）（1250万个SEA特异性变异对1180万个1KGP变异）基因分型数据集时，SEA特异性面板产生的高置信度变异比千人基因组计划更多。此外，与TOPMED和人类基因组多样性项目相比，SEA特异性面板在OA基因分型数据集上推算的单核苷酸多态性（SNP）具有更好的估计质量分数（INFO、DR2和R），但在SGVP数据集上表现相似。该面板还表现出更高的召回率和非参考不一致率，表明参考面板的祖先亲近度的影响。然而，我们注意到推算准确性可能会受到参考面板大小的影响。
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