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