Background: Single nucleotide polymorphisms (SNPs) can be used in clinical association studies to determine the contribution of genes to drug efficacy. The goal of this work was to evaluate the feasibility of using SNP information of the Han Chinese in Beijing (CHB) population from the HapMap database for clinical association studies in the Taiwanese (TWN) population.
Methods: We compared the HapMap populations with our TWN study population with regard to allele frequencies for common SNPs in two candidate genes for antidepressant treatment response to determine the applicability of the HapMap CHB data for SNP selection in the TWN population.
Results and conclusion: Our preliminary results suggest that there was no significant difference, in terms of allele and haplotype frequencies, between the CHB population of the HapMap database and the TWN population collected by Vita Genomics Inc. Therefore, it is possible to use the CHB population of the HapMap database for SNP selection in association studies for the TWN population. Using haplotype analysis, we generated a panel of SNPs that may be strongly relevant to antidepressant response in this population.
Haplotype Frequency Haplotype Block Common SNPs BDNF Gene Antidepressant Response
This is a preview of subscription content, log in to check access
The authors extend their sincere appreciation to Vita Genomics Inc. for funding the research. The authors have no conflicts of interest that are directly relevant to the content of this study.
Serretti A, Artioli P. The pharmacogenomics of selective serotonin reuptake inhibitors. Pharmacogenomics 2004; 4: 233–44CrossRefGoogle Scholar
Murphy GM, Kremer C, Rodrigues HE, et al. Pharmacogenetics of antidepressant medication intolerance. Am J Psychiatry 2003; 160: 1830–5PubMedCrossRefGoogle Scholar
Peters EJ, Slager SL, McGrath PJ, et al. Investigation of serotonin-related genes in antidepressant response. Mol Psychiatry 2004; 9: 879–89PubMedCrossRefGoogle Scholar
Gabriel SB, Schaffner SF, Nguyen H, et al. The structure of haplotype blocks in the human genome. Science 2002; 296: 2225–9PubMedCrossRefGoogle Scholar
Hinds DA, Stuve LL, Nilsen GB, et al. Whole-genome patterns of common DNA variation in three human populations. Science 2005; 307: 1072–9PubMedCrossRefGoogle Scholar
The International HapMap Consortium. The International HapMap Project. Nature 2003; 426: 789–94CrossRefGoogle Scholar
Nibuya M, Morinobu S, Duman RS. Regulation of BDNF and trkB mRNA in rat brain by chronic electroconvulsive seizure and antidepressant drug treatments. J Neurosci 1995 Nov; 15(11): 7539–47PubMedGoogle Scholar
Tsai SJ, Cheng CY, Yu YW, et al. Association study of a brain-derived neurotrophic-factor genetic polymorphism and major depressive disorders, symptomatology, and antidepressant response. Am J Med Genet B Neuropsychiatr Genet 2003 Nov 15; 123(1): 19–22CrossRefGoogle Scholar
Serretti A, Zanardi R, Rossini D, et al. Influence of tryptophan hydroxylase and serotonin transporter genes on fluvoxamine antidepressant activity. Mol Psychiatry 2001; 6: 586–92PubMedCrossRefGoogle Scholar
Serretti A, Zanardi R, Cusin C, et al. Tryptophan hydroxylase gene associated with paroxetine antidepressant activity. Eur Neuropsychopharmacol 2001; 11: 375–80PubMedCrossRefGoogle Scholar
Gizatullin R, Zoboli G, Jonsson EG, et al. Haplotype analysis reveals tryptophan hydroxylase (TPH) 1 gene variants associated with major depression. Biol Psychiat 2006; 59(4): 295–300PubMedCrossRefGoogle Scholar
Wang N, Akey JM, Zhang K, et al. Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am J Hum Genet 2002; 71: 1227–34PubMedCrossRefGoogle Scholar
Barrett JC, Fry B, Mailer J, et al. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005; 21: 263–5PubMedCrossRefGoogle Scholar
Devlin B, Risch N. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995; 29(2): 311–22PubMedCrossRefGoogle Scholar