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Unraveling Ambiguous NAT2 Genotyping Data

¹ Department of Pharmacology, Medical School, University of Extremadura, Badajoz, Spain;² Institute for Occupational Physiology (IfADo), University of Dortmund, Dortmund, Germany;³ Fakultät Statistik, Technische Universität Dortmund, Dortmund, Germany;⁴ Department of Biochemistry and Molecular Biology, School of Biological Sciences, University of Extremadura, Badajoz, Spain;

^aaddress correspondence to this author at: Department of Pharmacology, Medical School, University of Extremadura, Avda. de Elvas s/n, 06071-Badajoz, Spain. Fax +34 24 27 94 58; e-mail jagundez{at}unex.es.

Abstract

Background: Arylamine N-acetyltransferase 2 (CoASAc; NAT2, EC 2.3.1.5) is a drug-metabolizing enzyme that displays common polymorphisms leading to impaired drug metabolism and adverse drug effects. Determination of the N-acetyltransferase 2 (arylamine N-acetyltransferase) (NAT2) genotype in clinical practice is hampered by the occurrence of ambiguous haplotype combinations that may lead to patient misclassification. We determined the frequencies for ambiguous NAT2 haplotypes and diplotypes in a white population and investigated the use of PHASE v2.1.1, a statistical program for haplotype reconstruction, to clarify this ambiguity and classify individuals according to their acetylation status.

Methods: By means of allele-specific haplotype mapping and sequencing, we determined the haplotypes for 7 common single-nucleotide polymorphisms in the NAT2 gene (n = 2624 haplotypes). To test the performance of PHASE, actual genotypes were deconstructed and then reconstructed by haplotype prediction.

Results: We identified 21 NAT2 allelic variants, including a new variant allele that combines the single-nucleotide polymorphisms rs1801279, rs1799929, and rs1208. In contrast, the previously described variant alleles *5G, *5J, *6E, *7A, *11A, *11B, and *14B were not identified in the study population. Ambiguous haplotypes were observed in 98 alleles (3.7%), and ambiguous diplotypes were observed in 64 individuals (4.9%). Eleven individuals (0.8%) were misclassified by the use of haplotype prediction.

Conclusions: Ambiguous NAT2 genotyping data are common. Actual NAT2 genotypes cannot be fully determined by haplotype prediction techniques. This study provides real haplotype data that can be used as a guide to convert NAT2 haplotypes and diplotypes into actual genotypes in white individuals.