Figure 3

Haplotypic diversity in COMT, ERCC1, FDPS and GRIK4. SNPs genotyped in Singapore Genome Variation Project (SGVP), HapMap and the absorption, distribution, metabolism and excretion (ADME) genotyping panel are shown in black vertical lines with respect to their genomic positions. In panel a, the haplotypes carrying the risk allele of COMT rs9332377 (T allele), which is associated with cisplatin-induced ototoxicity, are shown. Only the linkage disequilibrium (LD) block in which rs9332377 is located is shown. The Chinese population is not shown as there were no haplotypes containing the T allele observed in that population. In panel b, the haplotypes carrying the risk allele of ERCC1 rs11615 (A allele), which is associated with a higher risk of toxicity with platinum compounds, are shown. In panel c, haplotypes carrying the risk allele of FDPS rs2297480 (G allele), which is associated with decreased bisphosphonate response, are shown. In panel d, the haplotypes carrying the risk allele of GRIK4 rs1954787 (T allele), which is associated with decreased citalopram response, are shown. Regions were chosen such that haplotypes with frequency >1% accounted for at least 90% of all haplotypes. GRIK4 rs1954787 is located between two LD blocks and no region spanning both the left and right of the SNP contained haplotypes common enough to represent graphically. Only the region to the right of the SNP is shown but similar diversity exists on the left (data not shown). For all genes, only SNPs with minor allele frequency (MAF) ⩾0.05 were used for haplotype construction and only haplotypes with frequencies of at least 1% are shown, except for the COMT rs9332377 haplotype in Malay (MAS), which is the only haplotype in that population that carries the risk allele (a). SNPs that contain information in only one population are not shown. For COMT and GRIK4, the red boxes indicate the gene regions for which the haplotypes are shown. CHS, Chinese; INS, Indians.

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