Singapore Genome Variation Project: A haplotype map of three South-East Asian populations
- Yik Ying Teo1,
- Xueling Sim1,
- Rick TH Ong1,
- Adrian KS Tan2,
- Jieming Chen2,
- Erwin Tantoso2,
- Kerrin S Small3,
- Chee Seng Ku1,
- Edmund JD Lee1,
- Mark Seielstad2 and
- Kee Chia1,4
- 1 National University of Singapore;
- 2 Genome Institute of Singapore;
- 3 Wellcome Trust Centre for Human Genetics
- * Corresponding author; email: ephcks{at}nus.edu.sg
Abstract
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 South-East Asia. This online database catalogues 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.
Footnotes
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- Received April 15, 2009.
- Accepted August 10, 2009.
- Copyright © 2009, Cold Spring Harbor Laboratory Press
