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Determination of novel CYP2D6 haplotype using the targeted sequencing followed by the long-read sequencing and the functional characterization in the Japanese population

Journal of Human Genetics volume 66, pages 139–149 (2021)Cite this article

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Abstract

Next-generation sequencing (NGS) has identified variations in cytochrome P450 (CYP) 2D6 associated with drug responses. However, determination of novel haplotypes is difficult because of the short reads generated by NGS. We aimed to identify novel CYP2D6 variants in the Japanese population and predict the CYP2D6 phenotype based on in vitro metabolic studies. Using a targeted NGS panel (PKSeq), 990 Japanese genomes were sequenced, and then novel CYP2D6 haplotypes were determined. Km, Vmax, and intrinsic clearance (Vmax/Km) of N-desmethyl-tamoxifen 4-hydroxylation were calculated by in vitro metabolic studies using cDNA-expressed CYP2D6 proteins. After determination of the CYP2D6 diplotypes, phenotypes of the individuals were predicted based on the in vitro metabolic activities. Targeted NGS identified 14 CYP2D6 variants not registered in the Pharmacogene Variation Consortium (PharmVar) database. Ten novel haplotypes were registered as CYP2D6*128 to *137 alleles in the PharmVar database. Based on the Vmax/Km value of each allele, *128, *129, *130, *131, *132, and *133 were predicted to be nonfunctional alleles. According to the results of the present study, six normal metabolizers (NM) and one intermediate (IM) metabolizers were designated as IM and poor metabolizers (PM), respectively. Our findings provide important insights into novel haplotypes and haplotypes of CYP2D6 and the effects on in vitro metabolic activities.

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Acknowledgements

We would like to thank Editage (www.editage.com) for English language editing. This study was supported by the Japan Agency for Medical Research and Development (AMED) under Grant Number JP19km0405201 and JP19kk0305009.

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Authors and Affiliations

  1. Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan

    Koya Fukunaga & Taisei Mushiroda

  2. Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan

    Eiji Hishinuma & Masahiro Hiratsuka

  3. Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan

    Eiji Hishinuma & Masahiro Hiratsuka

  4. Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan

    Eiji Hishinuma & Masahiro Hiratsuka

  5. Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan

    Masahiro Hiratsuka

  6. Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan

    Ken Kato

  7. Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan

    Takuji Okusaka

  8. Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan

    Takeo Saito, Masashi Ikeda & Nakao Iwata

  9. Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan

    Teruhiko Yoshida

  10. Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Cancer Institute, Tokyo, Japan

    Hitoshi Zembutsu

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  1. Koya Fukunaga
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Fukunaga, K., Hishinuma, E., Hiratsuka, M. et al. Determination of novel CYP2D6 haplotype using the targeted sequencing followed by the long-read sequencing and the functional characterization in the Japanese population. J Hum Genet 66, 139–149 (2021). https://doi.org/10.1038/s10038-020-0815-x

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