Haplotype-specific PCR for NAT2 diplotyping

Nuanjun Wichukchinda; Jirapa Pakdee; Punna Kunhapan; Wimala Imunchot; Licht Toyo-Oka; Katsushi Tokunaga; Surakameth Mahasirimongkol

doi:10.1038/s41439-020-0101-7

Haplotype-specific PCR for NAT2 diplotyping

Hum Genome Var. 2020 May 11:7:13. doi: 10.1038/s41439-020-0101-7. eCollection 2020.

Authors

Nuanjun Wichukchinda¹, Jirapa Pakdee¹, Punna Kunhapan¹, Wimala Imunchot¹, Licht Toyo-Oka^{2

3}, Katsushi Tokunaga^{2

4}, Surakameth Mahasirimongkol¹

Affiliations

¹ 1Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand.
² 2Department of Human Genetics, Graduates School of Medicine, The University of Tokyo, Tokyo, Japan.
³ 3Present Address: National Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan.
⁴ 4Present Address: Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan.

Abstract

N-acetyltransferase 2 (NAT2) is an enzyme that acetylates many kinds of drugs, including the antituberculosis drug isoniazid. The NAT2 gene is highly diverse across populations. An individual can be classified as having a slow acetylator (SA), an intermediate acetylator (IA), or a rapid acetylator (RA) phenotype based on its two haplotypes (diplotype) of NAT2. SA individuals are at a higher risk for isoniazid-induced hepatitis, while the RA phenotype contributes to failure in tuberculosis treatment. Being able to predict individual NAT2 phenotypes is important for dose adjustment of isoniazid. NAT2 haplotypes are commonly determined via an indirect method of statistical haplotype inference from SNP genotyping. Here, we report a direct NAT2 haplotyping method using haplotype-specific PCR (HS-PCR) for the 6 most commonly found NAT2 haplotypes: NAT2*4, NAT2*5B, NAT2*6A, NAT2*7B, NAT2*12A, and NAT2*13A. Validation of this HS-PCR method via comparison with a sequencing method in 650 Thai DNA samples (107 RA, 279 IA, and 264 SA samples) showed a concordance rate for diplotype calls of 99.23% (645/650 samples). The discordant results in 5 samples were due to 3 rare NAT2 haplotypes: NAT*5C (n = 3), NAT2*7C (n = 1), and NAT2*11A (n = 1). This novel HS-PCR method allows direct NAT2 diplotyping, enabling the implementation of NAT2 acetylator phenotypes in clinical pharmacogenetic testing.

Keywords: Predictive markers; Risk factors.