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

for the MENDEL study group

Research output: Contribution to journalArticle

Abstract

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

Original languageEnglish
JournalJournal of gastroenterology
DOIs
Publication statusAccepted/In press - 2019 Jan 1

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Codon
Genotype
Inflammatory Bowel Diseases
Haplotypes
DNA

Keywords

  • Inflammatory bowel disease
  • NUDT15
  • Pharmacogenetics
  • Thiopurines

ASJC Scopus subject areas

  • Gastroenterology

Cite this

@article{446dcc8d8a2c4604b2bede4d193bc16e,
title = "High-resolution melt analysis enables simple genotyping of complicated polymorphisms of codon 18 rendering the NUDT15 diplotype",
abstract = "Background: 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. Methods: 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. Results: 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. Conclusions: Our study showed that HRM method enables simple genotyping of complicated codon 18 variants essential to haplotype estimation of the NUDT15.",
keywords = "Inflammatory bowel disease, NUDT15, Pharmacogenetics, Thiopurines",
author = "{for the MENDEL study group} and Yoichi Kakuta and Yasuhiro Izumiyama and Daisuke Okamoto and Takeru Nakano and Ryo Ichikawa and Takeo Naito and Rintaro Moroi and Masatake Kuroha and Yoshitake Kanazawa and Tomoya Kimura and Hisashi Shiga and Hisaaki Kudo and Naoko Minegishi and Yosuke Kawai and Katsushi Tokunaga and Masao Nagasaki and Yoshitaka Kinouchi and Yasuo Suzuki and Atsushi Masasmune and Tetsuya Takagawa and Shiro Nakamura and Kentaro Ikeya and Hiroyuki Hanai and Hirotake Sakuraba and Atsushi Nishida and Akira Andoh and Shoko Nakagawa and Makoto Sasaki and Miki Miura and Tadakazu Hisamatsu and Takahiko Toyonaga and Taku Kobayashi and Kei Onodera and Hiroshi Nakase and Masaru Shinozaki and Yoh Ishiguro and Shinta Mizuno and Makoto Naganuma and Masahiro Takahara and Sakiko Hiraoka and Shunichi Yanai and Takayuki Matsumoto and Ryota Hokari and Tomoo Nakagawa and Hiroshi Araki and Satoshi Motoya and Shunji Ishihara and Naoki Oshima and Takehiko Katsurada and Yu Sasaki",
year = "2019",
month = "1",
day = "1",
doi = "10.1007/s00535-019-01638-x",
language = "English",
journal = "Journal of Gastroenterology",
issn = "0944-1174",
publisher = "Springer Japan",

}

TY - JOUR

T1 - High-resolution melt analysis enables simple genotyping of complicated polymorphisms of codon 18 rendering the NUDT15 diplotype

AU - for the MENDEL study group

AU - Kakuta, Yoichi

AU - Izumiyama, Yasuhiro

AU - Okamoto, Daisuke

AU - Nakano, Takeru

AU - Ichikawa, Ryo

AU - Naito, Takeo

AU - Moroi, Rintaro

AU - Kuroha, Masatake

AU - Kanazawa, Yoshitake

AU - Kimura, Tomoya

AU - Shiga, Hisashi

AU - Kudo, Hisaaki

AU - Minegishi, Naoko

AU - Kawai, Yosuke

AU - Tokunaga, Katsushi

AU - Nagasaki, Masao

AU - Kinouchi, Yoshitaka

AU - Suzuki, Yasuo

AU - Masasmune, Atsushi

AU - Takagawa, Tetsuya

AU - Nakamura, Shiro

AU - Ikeya, Kentaro

AU - Hanai, Hiroyuki

AU - Sakuraba, Hirotake

AU - Nishida, Atsushi

AU - Andoh, Akira

AU - Nakagawa, Shoko

AU - Sasaki, Makoto

AU - Miura, Miki

AU - Hisamatsu, Tadakazu

AU - Toyonaga, Takahiko

AU - Kobayashi, Taku

AU - Onodera, Kei

AU - Nakase, Hiroshi

AU - Shinozaki, Masaru

AU - Ishiguro, Yoh

AU - Mizuno, Shinta

AU - Naganuma, Makoto

AU - Takahara, Masahiro

AU - Hiraoka, Sakiko

AU - Yanai, Shunichi

AU - Matsumoto, Takayuki

AU - Hokari, Ryota

AU - Nakagawa, Tomoo

AU - Araki, Hiroshi

AU - Motoya, Satoshi

AU - Ishihara, Shunji

AU - Oshima, Naoki

AU - Katsurada, Takehiko

AU - Sasaki, Yu

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Background: 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. Methods: 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. Results: 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. Conclusions: Our study showed that HRM method enables simple genotyping of complicated codon 18 variants essential to haplotype estimation of the NUDT15.

AB - Background: 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. Methods: 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. Results: 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. Conclusions: Our study showed that HRM method enables simple genotyping of complicated codon 18 variants essential to haplotype estimation of the NUDT15.

KW - Inflammatory bowel disease

KW - NUDT15

KW - Pharmacogenetics

KW - Thiopurines

UR - http://www.scopus.com/inward/record.url?scp=85074281228&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85074281228&partnerID=8YFLogxK

U2 - 10.1007/s00535-019-01638-x

DO - 10.1007/s00535-019-01638-x

M3 - Article

C2 - 31641873

AN - SCOPUS:85074281228

JO - Journal of Gastroenterology

JF - Journal of Gastroenterology

SN - 0944-1174

ER -