Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations
Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations
复制标题
DOI：
10.1101/gr.095000.109
复制
发表时间：
2009-11-01
期刊：
影响因子：
7
通讯作者：
Chia, Kee-Seng
中科院分区：
文献类型：
--
作者：
Teo, Yik-Ying;Sim, Xueling;Chia, Kee-Seng
新加坡基因组变异计划（SGVP）提供了来自东南亚华人、马来人和印度人群体的268个个体的160万个单核苷酸多态性（snp）基因分型的公开资源。这个在线数据库以类似于国际HapMap项目的格式编目了基因型和分阶段单倍型数据的信息和摘要，包括等位基因频率、连锁不平衡（LD）评估和重组率。在这里，我们介绍了这一资源，并描述了基于HapMap和人类基因组多样性计划的汇总数据的人类基因组变异分析，为亚洲三个主要人口群体的人口结构提供了有用的见解。此外，该资源还调查了整个基因组中HapMap和SGVP群体之间LD区域模式的差异，并使用两个成熟的指标：his和XP-EHH来寻找积极自然选择的特征。原始的和处理过的遗传数据，连同所有的种群遗传摘要，都可以通过通用基因组浏览器模型的网络浏览器公开下载和浏览。
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.