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High-resolution melt analysis enables simple genotyping of complicated polymorphisms of codon 18 rendering the NUDT15 diplotype

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A Correction to this article was published on 25 November 2019

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The genetic variants of NUDT15 have been verified to induce adverse events (AEs) of thiopurines. Codon 139 variants are frequently observed in Asians, while multiple variants are seen in codon 18 which also cause AEs including the European ancestry. The purpose of this study is to establish a technique capable of the simple genotyping of NUDT15 codon 18 and to evaluate its efficacy.


A high-resolution melt (HRM) technique is performed to simply determine genotypes. The accuracy of HRM analysis was evaluated with DNAs from 1245 Japanese patients with inflammatory bowel diseases. Subsequently, another group of 572 patients was analyzed to verify the method. The diplotypes and the frequency of their AEs were estimated on the basis of codon 18 and 139 genotypes.


The HRM analysis enabled the correct identification of the three main genotypes, ref/ref, ref/ins, and ref/V18I, in 1236 of 1241 cases. All rare genotypes including ref/del were identified as the impossible-to-determine group, the proper diagnosis rate was 99.6%. In the verification test using other samples, the diagnosis rate was 99.7%. By estimating diplotypes using both codon 18 and 139 genotypes, 2.74% and 2.13% of Japanese patients with Arg/Arg and Arg/Cys of codon 139 have a lower enzymatic activity of NUDT15 and a higher risk for adverse responses than those estimated by codon 139 genotypes alone.


Our study showed that HRM method enables simple genotyping of complicated codon 18 variants essential to haplotype estimation of the NUDT15.

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  • 25 November 2019

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Inflammatory bowel disease


Ulcerative colitis


Crohn’s disease


Behçet’s disease






Adverse event


White blood cell


High-resolution melt


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We would like to thank all of the patients who participated in this study. This research was supported by AMED under Grant Number 18kk0305002 and 19ek0410056 to Y. Kakuta, and 16km0405205h0101 to M. Nagasaki. This work was supported in part by the Tohoku Medical Megabank Project (Special Account for Reconstruction from the Great East Japan Earthquake). Some of the computational resources were provided by the ToMMo supercomputer system.

Members of MENDEL study group [name and affiliation] are: Tetsuya Takagawa and Shiro Nakamura [Division of Internal Medicine, Department of Inflammatory Bowel Disease, Hyogo College of Medicine, Nishinomiya, Japan], Kentaro Ikeya and Hiroyuki Hanai [Centre for Gastroenterology and Inflammatory Bowel Disease Research, Hamamatsu South Hospital, Hamamatsu, Japan], Hirotake Sakuraba [Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan], Atsushi Nishida and Akira Andoh [Department of Gastroenterology, Shiga University of Medical Science, Otsu, Japan], Shoko Nakagawa and Makoto Sasaki[Division of Gastroenterology, Department of Internal Medicine, Aichi Medical University School of Medicine, Aichi, Japan], Miki Miura and Tadakazu Hisamatsu [The Third Department of Internal Medicine, Kyorin University School of Medicine, Mitaka, Japan], Takahiko Toyonaga and Taku Kobayashi [Center for Advanced IBD Research and Treatment, Kitasato University Kitasato Institute Hospital, Tokyo, Japan], Kei Onodera and Hiroshi Nakase [Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan], Masaru Shinozaki [Department of Surgery, IMSUT Hospital, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan], Yoh Ishiguro [Department of Gastroenterology and Hematology, Hirosaki National Hospital, Hirosaki, Japan], Shinta Mizuno and Makoto Naganuma [Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan], Masahiro Takahara and Sakiko Hiraoka [Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan], Shunichi Yanai and Takayuki Matsumoto[Division of Gastroenterology, Department of Internal Medicine, School of Medicine, Iwate Medical University, Morioka, Japan], Ryota Hokari [Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Defense Medical College, Tokorozawa, Japan], Tomoo Nakagawa[Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan], Hiroshi Araki [Division of Endscopy, Gifu University Hospital, Gifu, Japan], Satoshi Motoya [IBD Center, Sapporo-Kosei General Hospital, Sapporo, Japan], Shunji Ishihara and Naoki Oshima [Department of Internal Medicine II, Shimane University Faculty of Medicine, Shimane, Japan.], Takehiko Katsurada [Department of Gastroenterology and Hepatology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.], Yu Sasaki [Department of Gastroenterology, Yamagata University Faculty of Medicine, Yamagata, Japan.], Takafumi Otsuka [Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan.], Mikihiro Fujiya [Department of Medicine, Division of Gastroenterology and Hematology/Oncology, Asahikawa Medical University, Asahikawa, Japan.], Motoyuki Onodera [Department of Gastroenterology, Iwate Prefectural Isawa Hospital, Iwate, Japan.], Masakazu Nagahori and Katsuyoshi Matsuoka [Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan.], Katsuhiro Arai [Division of Gastroenterology, National Center for Child Health and Development, Setagaya, Tokyo, Japan.], Yuichiro Sato [Department of Gastroenterology, Osaki Citizen Hospital, Osaki, Japan.], Mitsunori Noguchi [Noguchi Clinic, Sendai, Japan], Minoru Matsuura [Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Japan.], Tomoaki Ishikawa, Hiroki Nakajima and Hiroshi Terasaki [LSI Medience Corporation, Japan], Yukiko Abe [G&G Science Co., Ltd.] and Mai Kato [MENDEL study secretariat].

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YI, Y. Kakuta, DO and Y. Kinouchi designed the study. YI, Y. Kakuta, T. Naito, Y. Kawai, and MN acquired data. YI, Y. Kakuta, DO, T. Nakano, RI, RM, MK, HS, Y. Kanazawa, TK, and KN recruited patients. HK and NM managed the biobank samples. YI, Y. Kakuta, DO, Y. Kawai, KT and MN analyzed data. YI, Y. Kakuta, DO, Y. Kinouchi, YS and AM drafted the manuscript.

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Correspondence to Yoichi Kakuta.

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The members of the MENDEL study group are listed in acknowledgements section.

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Kakuta, Y., Izumiyama, Y., Okamoto, D. et al. High-resolution melt analysis enables simple genotyping of complicated polymorphisms of codon 18 rendering the NUDT15 diplotype. J Gastroenterol 55, 67–77 (2020).

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