Unraveling ambiguous NAT2 genotyping data

Clin Chem. 2008 Aug;54(8):1390-4. doi: 10.1373/clinchem.2008.105569.


Background: Arylamine N-acetyltransferase 2 (CoASAc; NAT2, EC 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arylamine N-Acetyltransferase / genetics*
  • Computational Biology* / methods
  • Computational Biology* / statistics & numerical data
  • Gene Frequency
  • Genotype
  • Humans
  • Polymorphism, Single Nucleotide / genetics*
  • White People


  • Arylamine N-Acetyltransferase
  • NAT2 protein, human