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

IF 4.7 2区医学 Q1 GENETICS & HEREDITY

NPJ Genomic Medicine Pub Date : 2024-10-05 DOI:10.1038/s41525-024-00435-7

Alvin Cengnata, Lian Deng, Wai-Sum Yap, Lay-Hong Renee Lim, Chee-Onn Leong, Shuhua Xu, Boon-Peng Hoh

{"title":"A genotype imputation reference panel specific for native Southeast Asian populations.","authors":"Alvin Cengnata, Lian Deng, Wai-Sum Yap, Lay-Hong Renee Lim, Chee-Onn Leong, Shuhua Xu, Boon-Peng Hoh","doi":"10.1038/s41525-024-00435-7","DOIUrl":null,"url":null,"abstract":"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 R2) 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.","PeriodicalId":19273,"journal":{"name":"NPJ Genomic Medicine","volume":"9 1","pages":"47"},"PeriodicalIF":4.7000,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11455956/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"NPJ Genomic Medicine","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1038/s41525-024-00435-7","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}

引用次数: 0

Abstract

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 R²) 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.

查看原文本刊更多论文

专门针对东南亚本地人群的基因型推算参考面板。

我们报告了通过 "跨面板推算 "方法建立的 "东南亚特异性（SEA-specific）参考面板"，该面板由来自 GA100K、SG10K 和马来西亚半岛猩猩（OA）数据集的 2550 个样本组成，涵盖 113,851,450 个变异。与千人基因组计划（1000 Genomes Project，1KGP）基因分型数据集（890 万 SEA 特异性样本 vs 810 万 1KGP 样本）和新加坡基因组变异计划（Singapore Genome Variation Project，SGVP）基因分型数据集（1250 万 SEA 特异性样本 vs 1180 万 1KGP 样本）相比，SEA 特异性面板产生了更多的高置信度变异。此外，与 TOPMED 和人类基因组多样性项目相比，在 OA 基因分型数据集上，东南亚特异性面板估算的 SNPs 质量分数（INFO、DR2 和 R2）更高，但在 SGVP 数据集上的表现类似。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缘关系的影响。不过，我们注意到，参照面板的大小可能会影响估算的准确性。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

NPJ Genomic Medicine Biochemistry, Genetics and Molecular Biology-Molecular Biology

CiteScore

9.40

自引率

1.90%

发文量

审稿时长

17 weeks

期刊介绍： npj Genomic Medicine is an international, peer-reviewed journal dedicated to publishing the most important scientific advances in all aspects of genomics and its application in the practice of medicine. The journal defines genomic medicine as "diagnosis, prognosis, prevention and/or treatment of disease and disorders of the mind and body, using approaches informed or enabled by knowledge of the genome and the molecules it encodes." Relevant and high-impact papers that encompass studies of individuals, families, or populations are considered for publication. An emphasis will include coupling detailed phenotype and genome sequencing information, both enabled by new technologies and informatics, to delineate the underlying aetiology of disease. Clinical recommendations and/or guidelines of how that data should be used in the clinical management of those patients in the study, and others, are also encouraged.