来自用户 吴建虎 的文献。
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吴建虎
(2022-02-28 11:32):
#paper doi:10.1016/j.cell.2019.09.019 Cell 2019 Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore SG10K pilot study
一共4810个WGS样本:Chinese：2,780，Malay：903，Indian：1,127 ，平均深度：13.7X，从常染色体以及X染色体中一共找到89.16M的SNPs和9.11M的indels。文章将重点放在了群体结构分析上，同时对于低深度测序结果的校正上给定了一个新的思路。SG10K 数据库丰富了东亚和南亚人群的基因型，结合1KGP数据库可以很好的对Imputation结果进行校正。根据群体结构分析发现Malay人可能将是SG10K的亮点，这对于CDX人群分析提供了新的帮助。
个人感觉：文章仍有一些不足之处，比如关于假阳性的问题没有正面回答，让人对于后续的分析结果产生疑问。
Abstract:
Underrepresentation of Asian genomes has hindered population and medical genetics research on Asians, leading to population disparities in precision medicine. By whole-genome sequencing of 4,810 Singapore Chinese, Malays, and Indians, …
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Underrepresentation of Asian genomes has hindered population and medical genetics research on Asians, leading to population disparities in precision medicine. By whole-genome sequencing of 4,810 Singapore Chinese, Malays, and Indians, we found 98.3 million SNPs and small insertions or deletions, over half of which are novel. Population structure analysis demonstrated great representation of Asian genetic diversity by three ethnicities in Singapore and revealed a Malay-related novel ancestry component. Furthermore, demographic inference suggested that Malays split from Chinese ∼24,800 years ago and experienced significant admixture with East Asians ∼1,700 years ago, coinciding with the Austronesian expansion. Additionally, we identified 20 candidate loci for natural selection, 14 of which harbored robust associations with complex traits and diseases. Finally, we show that our data can substantially improve genotype imputation in diverse Asian and Oceanian populations. These results highlight the value of our data as a resource to empower human genetics discovery across broad geographic regions.
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