| Summary: | <p>Abstract</p> <p>Background</p> <p>In order to provide a cost-effective tool to analyse pharmacogenetic markers in malaria treatment, DNA microarray technology was compared with sequencing of polymerase chain reaction (PCR) fragments to detect single nucleotide polymorphisms (SNPs) in a larger number of samples.</p> <p>Methods</p> <p>The microarray was developed to affordably generate SNP data of genes encoding the human cytochrome P450 enzyme family (<it>CYP</it>) and <it>N</it>-acetyltransferase-2 (<it>NAT2</it>) involved in anti-malarial drug metabolisms and with known polymorphisms, i.e. <it>CYP2A6, CYP2B6</it>, <it>CYP2C8</it>, <it>CYP2C9</it>, <it>CYP2C19</it>, <it>CYP2D6</it>, <it>CYP3A4</it>, <it>CYP3A5</it>, and <it>NAT2</it>.</p> <p>Results</p> <p>For some SNPs, i.e. <it>CYP2A6*2</it>, <it>CYP2B6*5</it>, <it>CYP2C8*</it>3, <it>CYP2C9*3/*5</it>, <it>CYP2C19*3</it>, <it>CYP2D6*4 </it>and <it>NAT2*6/*7/*14</it>, 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. <it>CYP2D6*17 </it>(2850C>T), <it>CYP3A4*1B </it>and CYP3A5*3.</p> <p>Conclusion</p> <p>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.</p>
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