Centre for Molecular Epidemiology, National University of Singapore, Singapore 117597.
Genome Res. 2009 Nov;19(11):2154-62. doi: 10.1101/gr.095000.109. Epub 2009 Aug 21.
The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.
新加坡基因组变异计划 (SGVP) 提供了一个公开的资源，其中包括在东南亚的华人、马来人和印度人群体的 268 个人中进行的 160 万个单核苷酸多态性 (SNP) 基因分型。这个在线数据库以类似于国际人类基因组单体型图计划的格式，对基因型和相位单倍型数据的信息和摘要进行编目，包括等位基因频率、连锁不平衡 (LD) 的评估和重组率。在这里，我们介绍了这个资源，并描述了对 HapMap 和人类基因组多样性计划的数据进行聚合分析的结果，为亚洲三大人群的人口结构提供了有用的见解。此外，该资源还在全基因组范围内调查了 HapMap 和 SGVP 人群之间 LD 的区域模式的变异，并使用两种成熟的指标：iHS 和 XP-EHH，对自然选择的正选择信号进行了检测。原始和处理后的遗传数据，以及所有的群体遗传摘要，都可以通过一个基于通用基因组浏览器建模的网络浏览器进行下载和浏览。
