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.

Hans-Peter Rihs, Andrea John, Michael Scherenberg, Albrecht Seidel, Thomas Brüning

Index: Clin. Chim. Acta 376(1-2) , 240-3, (2007)

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Abstract

The utility of typing single nucleotide polymorphisms (SNPs) for the determination of the N-acetyltransferase 2 (NAT2) acetylation status is a matter of debate.Evaluation of the concordance between deduced genotype results of seven human NAT2 SNPs generated by Real-time PCR analysis and human NAT2 phenotypes.NAT2 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).Phenotypic 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 (>or=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.