title: Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations.
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 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.
authors.affiliation: Centre for Molecular Epidemiology, National University of Singapore, Singapore 117597.
authors.forename: Yik-Ying
authors.initials: YY
authors.lastname: Teo
authors.forename: Xueling
authors.initials: X
authors.lastname: Sim
authors.forename: Rick T H
authors.initials: RT
authors.lastname: Ong
authors.forename: Adrian K S
authors.initials: AK
authors.lastname: Tan
authors.forename: Jieming
authors.initials: J
authors.lastname: Chen
authors.forename: Erwin
authors.initials: E
authors.lastname: Tantoso
authors.forename: Kerrin S
authors.initials: KS
authors.lastname: Small
authors.forename: Chee-Seng
authors.initials: CS
authors.lastname: Ku
authors.forename: Edmund J D
authors.initials: EJ
authors.lastname: Lee
authors.forename: Mark
authors.initials: M
authors.lastname: Seielstad
authors.forename: Kee-Seng
authors.initials: KS
authors.lastname: Chia
mesh_terms: D002681:China; D002874:Chromosome Mapping; D030541:Databases, Genetic; D005787:Gene Frequency; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population / Q000379:methods; D015894:Genome, Human / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D023281:Genomics / Q000379:methods; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D007194:India; D015810:Linkage Disequilibrium; D008296:Malaysia; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D012641:Selection, Genetic; D012846:Singapore
references.citation: Science. 2005 Dec 16;310(5755):1782-6
references.pmid: 16357253
references.citation: PLoS Genet. 2008 Feb;4(2):e32
references.pmid: 18282109
references.citation: PLoS Genet. 2007 Jul;3(7):e114
references.pmid: 17676998
references.citation: Cold Spring Harb Symp Quant Biol. 2003;68:69-78
references.pmid: 15338605
references.citation: Science. 2005 Oct 14;310(5746):321-4
references.pmid: 16224025
references.citation: Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11763-8
references.pmid: 9751739
references.citation: Nature. 2005 Oct 27;437(7063):1299-320
references.pmid: 16255080
references.citation: Am J Hum Genet. 2006 Apr;78(4):629-44
references.pmid: 16532393
references.citation: Diabetologia. 2008 Nov;51(11):2134-7
references.pmid: 18766326
references.citation: Nat Genet. 2005 Nov;37(11):1217-23
references.pmid: 16244653
references.citation: Nature. 2008 Feb 21;451(7181):998-1003
references.pmid: 18288195
references.citation: Nature. 2004 Sep 16;431(7006):302-5
references.pmid: 15372031
references.citation: Nat Genet. 2008 Oct;40(10):1253-60
references.pmid: 18776909
references.citation: Science. 2007 Jun 1;316(5829):1341-5
references.pmid: 17463248
references.citation: Science. 2008 Feb 22;319(5866):1100-4
references.pmid: 18292342
references.citation: Nature. 2007 Oct 18;449(7164):913-8
references.pmid: 17943131
references.citation: Diabetes. 2008 Oct;57(10):2834-42
references.pmid: 18633108
references.citation: Genet Epidemiol. 2009 Feb;33(2):128-35
references.pmid: 18814308
references.citation: PLoS Biol. 2006 Mar;4(3):e72
references.pmid: 16494531
references.citation: Nat Genet. 2006 Jun;38(6):663-7
references.pmid: 16715096
references.citation: Nat Genet. 2006 Nov;38(11):1298-303
references.pmid: 17057720
references.citation: Science. 2007 Jun 1;316(5829):1331-6
references.pmid: 17463246
references.citation: Bioinformatics. 2005 Jan 15;21(2):263-5
references.pmid: 15297300
references.citation: Clin Pharmacol Ther. 2006 Mar;79(3):197-205
references.pmid: 16513444
references.citation: Bioinformatics. 2005 May 1;21(9):1958-63
references.pmid: 15657097
references.citation: Clin Pharmacokinet. 2006;45(12):1189-200
references.pmid: 17112295
references.citation: Nature. 2007 Oct 18;449(7164):851-61
references.pmid: 17943122
references.citation: Nat Genet. 2006 Feb;38(2):214-7
references.pmid: 16429162
references.citation: Nat Genet. 2009 Jun;41(6):657-65
references.pmid: 19465909
references.citation: Science. 2002 Dec 20;298(5602):2381-5
references.pmid: 12493913
references.citation: Nat Genet. 2006 Nov;38(11):1251-60
references.pmid: 17057719
references.citation: Diabetes. 2008 Aug;57(8):2226-33
references.pmid: 18469204
references.citation: Ann Eugen. 1951 Mar;15(4):323-54
references.pmid: 24540312
references.citation: Nat Genet. 2006 Aug;38(8):904-9
references.pmid: 16862161
references.citation: Genome Res. 2009 Oct;19(10):1849-60
references.pmid: 19541915
references.citation: Nat Genet. 2007 Jul;39(7):906-13
references.pmid: 17572673
references.citation: Nature. 2007 Jun 7;447(7145):655-60
references.pmid: 17554299
references.citation: Diabetes. 2009 Feb;58(2):493-8
references.pmid: 19033397
references.citation: Genet Epidemiol. 2010 Jan;34(1):34-41
references.pmid: 19479748
references.citation: Nat Genet. 2007 Jun;39(6):770-5
references.pmid: 17460697
references.citation: Biotechniques. 2002 Jun;Suppl:56-8, 60-1
references.pmid: 12083399
references.citation: Am J Hum Genet. 2009 Feb;84(2):235-50
references.pmid: 19215730
references.citation: Science. 2007 Jun 1;316(5829):1336-41
references.pmid: 17463249