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SHORT COMMUNICATION

© 2006 Adis Data Information BV. All rights reserved.

A Case Study of the Utility of the HapMap Database for Pharmacogenomic Haplotype Analysis in the Taiwanese Population Eugene Lin,1 Yuchi Hwang1 and Chi-Meng Tzeng1,2 1 2

Vita Genomics Inc., Taipei, Taiwan GeneCore BioTechnologies Co. Ltd, Shanghai, China

Abstract

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.

Background Depression is the most common psychiatric disorder worldwide. No single antidepressant has been shown to be more effective than any other in lifting depression, and the effectiveness of any particular antidepressant in an individual is difficult to predict. Thus, doctors must prescribe antidepressants based on trial and error. Evidence is accumulating to suggest that the efficacy of antidepressants results from the combined effects of a number of genetic variants, such as single nucleotide polymorphisms (SNPs).[1] Although there are not enough data currently available to prove this hypothesis, more and more genetic variants associated with antidepressant response are being discovered.[1-3] In clinical association studies, SNPs can be used to understand the relationship between genetic variations and drug efficacy by comparing SNPs found in responders to a particular drug with those found in non-responders.[1] However, it would be extremely

inefficient to test all of the 10 million common SNPs found in an individual’s chromosomes. Genotypes at many of these sites are strongly correlated because genetic variants that are close to each other on the chromosome are often inherited together.[4,5] These regions of linked variants are known as haplotypes. Thus, it is not necessary to assay all common SNPs if we can obtain the patterns of haplotypes between common SNPs. In this work, we utilized the HapMap database[6] to gain haplotype information in order to identify SNPs that may be relevant to the drug efficacy of antidepr