Concordance between the deduced acetylation status generated by high-speed Real-time PCR based NAT2 genotyping of seven single nucleotide polymorphisms and human NAT2 phenotypes determined by a caffeine assay

BackgroundThe utility of typing single nucleotide polymorphisms (SNPs) for the determination of the N-acetyltransferase 2 (NAT2) acetylation status is a matter of debate.Aims of the studyEvaluation of the concordance between deduced genotype results of seven human NAT2 SNPs generated by Real-time PCR analysis and human NAT2 phenotypes.MethodsNAT2 phenotypes of 38 Caucasian workers were determined using a suitable caffeine test method. Genomic DNA aliquots were used for the determination of seven human NAT2-specific SNPs (G191A, C282T, T341C, C481T, G590A, A803G, G857A).Results and conclusionsPhenotypic results based on the molar ratio of 5-acetylamino-6-formylamino-3-methyluracil (AFMU)/(AFMU + 1-methlyuric acid (1U) + 1-methylxanthine (1X)) calculated from excreted caffeine metabolite levels in urine samples with 0.3 as a cut-off point between slow (< 0.3) and rapid acetylators (≥ 0.3). Twenty-seven samples belonged to the slow (mean 0.13; range: 0.03–0.25), 11 to the rapid (mean: 0.41; range: 0.34–0.48) acetylators. LightCycler™ analyses revealed 11 different NAT2 variant combinations, whereby ⁎5B/⁎5B and ⁎5B/⁎6A or ⁎5A/⁎6C (each 21%), were the most frequent. The deduced acetylation status of the seven NAT2 SNPs matched perfectly with the 38 results determined by phenotyping. This study showed a 100% concordance between NAT2 phenotypes and the deduced NAT2 genotypes and the suitability of the high-speed NAT2-specific LightCycler™ analysis in a Caucasian population.