A microarray-based system for the simultaneous analysis of single nucleotide polymorphisms in human genes involved in the metabolism of anti-malarial drugs

The microarray was developed to affordably generate SNP data of genes encoding the human cytochrome P450 enzyme family (CYP) and N-acetyltransferase-2 (NAT2) involved in anti-malarial drug metabolisms and with known polymorphisms, i.e. CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, and NAT2.For some SNPs, i.e. CYP2A6*2, CYP2B6*5, CYP2C8*3, CYP2C9*3/*5, CYP2C19*3, CYP2D6*4 and NAT2*6/*7/*14, agreement between both techniques ranged from substantial to almost perfect (kappa index between 0.61 and 1.00), whilst for other SNPs a large variability from slight to substantial agreement (kappa index between 0.39 and 1.00) was found, e.g. CYP2D6*17 (2850C>T), CYP3A4*1B and CYP3A5*3.The major limit of the microarray technology for this purpose was lack of robustness and with a large number of missing data or with incorrect specificity.Drug action depends on how drugs are metabolized and differences in activity of metabolizing enzymes can significantly contribute to the efficacy of drugs [1,2]. This might also be true for drugs given to treat malaria. The objective was to analyse single nucleotide polymorphisms (SNPs) in genes encoding enzymes implicated in metabolizing anti-malarial drugs in order to determine the contribution of these enzymes to the pharmacokinetics of the specific drugs. There are many methods available for the detection of SNPs (for review see [3,4]). These methods are either based on allele-specific hybridization or on primer extension reaction. Many of these techniques are time consuming, expensive and/or not suitable for use in resource-poor countries. Previously, a cost-effective DNA microarray-based [5] technique to detect SNPs associated with drug resistance in malaria parasites in a larger sample size has been developed and successfully used. To test whether this system also could be used for SNP determination in metabolizing enzyme genes, microarray determined SNPs were compared with sequencing. For this, a microarray was develope