Evaluation of resequencing on number of tag SNPs of 13 atherosclerosis-related genes in Thai population.
In the candidate gene approach, information about the distribution of single nucleotide polymorphisms (SNPs) is a crucial requirement for choosing efficient markers necessary for a case-control association study. To obtain such information, we discovered SNPs in 13 genes related to atherosclerosis by resequencing exon-flanking regions of 32 healthy Thai individuals. In total, 194 polymorphisms were identified, 184 of them SNPs, four insertions, and the rest deletions. Fifty-nine of the SNPs were characterized as novel polymorphisms, and these accounted for 30% of the identified SNPs. Comparing allele frequency distributions of the Thai population with other Asian populations shows similar patterns. In contrast, a low correlation pattern (r = 0.521) was found when comparing with either Caucasian or African populations. However, some rare alleles (rs11574541 and rs10874913) are found in the Thai population but not in other Asian populations. Most of the novel SNPs found were located outside the haplotype blocks generated by known SNPs in the Thai population. Only 5.77% of the novel SNPs lies in these defined haplotype blocks. The selection of haplotype-tagging SNPs shows that 8 of 13 genes benefited from the ethnic-specific genotype information. That is, when at least one novel SNP was present, the tagging SNPs chosen were altered. Functional prediction of 16 nonsynonymous SNPs (nsSNPs) by three different algorithm tools demonstrated that five nsSNPs possibly alter their corresponding protein functions. These results provide necessary information for conducting further genetic association studies involving the Thai population and demonstrate that resequencing of candidate genes provides more complete information for full genetic studies.
Centre National de Génotypage, 2 rue Gaston Crémieux, CP 5721, 91057, Evry Cedex, France. chintaphol@hotmail.com.|Chulabhorn Cancer Centre, Viphavadee-Rangsit road, Laksi, Bangkok, 10120, Thailand. chintaphol@hotmail.com.
Chintana
C
Tocharoentanaphol
Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.|Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Somying
S
Promso
Centre National de Génotypage, 2 rue Gaston Crémieux, CP 5721, 91057, Evry Cedex, France.
Dianna
D
Zelenika
Centre National de Génotypage, 2 rue Gaston Crémieux, CP 5721, 91057, Evry Cedex, France.|Research center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
Tassanee
T
Lowhnoo
National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand.
Sissades
S
Tongsima
Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
Thanyachai
T
Sura
Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
Wasun
W
Chantratita
Centre National de Génotypage, 2 rue Gaston Crémieux, CP 5721, 91057, Evry Cedex, France.
Fumihiko
F
Matsuda
Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
Sean
S
Mooney
Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.|Laboratoire de Génétique de la réponse aux infections chez l'homme, Institut Pasteur, 75724, Paris Cedex 15, France.
Anavaj
A
Sakuntabhai
D050197:Atherosclerosis / Q000208:ethnology / Q000235:genetics*; D044383:Black People; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D016324:Sequence Tagged Sites; D013785:Thailand