1
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Hozawa A, Nakaya K, Nakaya N, Nakamura T, Kogure M, Hatanaka R, Chiba I, Kanno I, Sugawara J, Kodama E, Hamanaka Y, Kobayashi T, Uruno A, Tsuchiya N, Hirata T, Narita A, Tsuboi A, Tamahara T, Otsuki A, Goto M, Taira M, Shimizu R, Suzuki K, Obara T, Kikuya M, Metoki H, Ishikuro M, Danjoh I, Ogishima S, Nagaie S, Minegishi N, Hiratsuka M, Kumada K, Nishijima I, Nobukuni T, Yamaguchi-Kabata Y, Nagami F, Kure S, Fuse N, Kinoshita K, Izumi Y, Kuriyama S, Yamamoto M. Progress report of the Tohoku Medical Megabank Community-Based Cohort Study: Study profile of the repeated center-based survey during second period in Miyagi Prefecture. J Epidemiol 2024:JE20230241. [PMID: 38403692 DOI: 10.2188/jea.je20230241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND The purpose of this study was to report the basic profile of the Miyagi Prefecture part of a repeated center-based survey during the second period (2nd period survey) of the Tohoku Medical Megabank Community-Based Cohort Study (TMM CommCohort Study), as well as the participants' characteristics based on their participation type in the baseline survey. METHODS The 2nd period survey, conducted from June 2017 to March 2021, included participants of the TMM CommCohort Study (May 2013 to March 2016). In addition to the questionnaire, blood, urine, and physiological function tests were performed during the 2nd period survey. There were three main ways of participation in the baseline survey: Type 1, Type 1 additional, or Type 2 survey. The 2nd period survey was conducted in the same manner as the Type 2 survey, which was based on the community support center (CSC). RESULTS In Miyagi Prefecture, 29,383 (57.7%) of 50,967 participants participated in the 2nd period survey. The participation rate among individuals who had visited the CSC was approximately 80%. Although some factors differed depending on the participation type in the baseline survey, the 2nd period survey respondents in the Type 1 and Type 2 survey groups at baseline had similar traits. CONCLUSIONS The 2nd period survey of the TMM CommCohort Study provided detailed follow-up information. Following up on the health conditions of the participants will clarify the long-term effects of disasters and contribute to personalized prevention.
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Affiliation(s)
- Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Kumi Nakaya
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Faculty of Data Science, Kyoto Women's University
| | - Mana Kogure
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Rieko Hatanaka
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Ippei Chiba
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Ikumi Kanno
- Graduate School of Medicine, Tohoku University
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Suzuki Memorial Hospital
| | - Eiichi Kodama
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Yohei Hamanaka
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Naho Tsuchiya
- Tohoku Medical Megabank Organization, Tohoku University
- Yamato Home Medical Care Clinic Kurihara
| | - Takumi Hirata
- Tohoku Medical Megabank Organization, Tohoku University
- Institute for Clinical and Translational Science, Nara Medical University Hospital
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Toru Tamahara
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Maki Goto
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Makiko Taira
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Masahiro Kikuya
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Department of Hygiene and Public Health, Teikyo University School of Medicine
| | - Hirohito Metoki
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Division of Public Health, Hygiene and Epidemiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Satoshi Nagaie
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Masahiro Hiratsuka
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Ichiko Nishijima
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Takahiro Nobukuni
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University
- Miyagi Children's Hospital
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Graduate School of Information Sciences, Tohoku University
- Institute of Development., aging, and cancer, Tohoku University
| | - Yoko Izumi
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- International Research Institute of Disaster Science, Tohoku University
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
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2
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Ohneda K, Hiratsuka M, Kawame H, Nagami F, Suzuki Y, Suzuki K, Uruno A, Sakurai-Yageta M, Hamanaka Y, Taira M, Ogishima S, Kuriyama S, Hozawa A, Tomita H, Minegishi N, Sugawara J, Danjoh I, Nakamura T, Kobayashi T, Yamaguchi-Kabata Y, Tadaka S, Obara T, Hishimuma E, Mano N, Matsuura M, Sato Y, Nakasone M, Honkura Y, Suzuki J, Katori Y, Kakuta Y, Masamune A, Aoki Y, Nakayama M, Kure S, Kinoshita K, Fuse N, Yamamoto M. A Pilot Study for Return of Individual Pharmacogenomic Results to Population-Based Cohort Study Participants. JMA J 2022; 5:177-189. [PMID: 35611229 PMCID: PMC9090545 DOI: 10.31662/jmaj.2021-0156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
Introduction: Pharmacogenomic (PGx) testing results provide valuable information on drug selection and appropriate dosing, maximization of efficacy, and minimization of adverse effects. Although the number of large-scale, next-generation-sequencing-based PGx studies has recently increased, little is known about the risks and benefits of returning PGx results to ostensibly healthy individuals in research settings. Methods: Single-nucleotide variants of three actionable PGx genes, namely, MT-RNR1, CYP2C19, and NUDT15, were returned to 161 participants in a population-based Tohoku Medical Megabank project. Informed consent was obtained from the participants after a seminar on the outline of this study. The results were sent by mail alongside sealed information letter intended for clinicians. As an exception, genetic counseling was performed for the MT-RNR1 m.1555A > G variant carriers by a medical geneticist, and consultation with an otolaryngologist was encouraged. Questionnaire surveys (QSs) were conducted five times to evaluate the participants’ understanding of the topic, psychological impact, and attitude toward the study. Results: Whereas the majority of participants were unfamiliar with the term PGx, and none had undergone PGx testing before the study, more than 80% of the participants felt that they could acquire basic PGx knowledge sufficient to understand their genomic results and were satisfied with their potential benefit and use in future prescriptions. On the other hand, some felt that the PGx concepts or terminology was difficult to fully understand and suggested that in-person return of the results was desirable. Conclusions: These results collectively suggest possible benefits of returning preemptive PGx information to ostensibly healthy cohort participants in a research setting.
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Affiliation(s)
- Kinuko Ohneda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masahiro Hiratsuka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Faculty of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Clinical Genetics, Jikei University Hospital, Tokyo, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Clinical Genetics, Ageo Central General Hospital, Ageo, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Yohei Hamanaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Makiko Taira
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- The United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Faculty of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Eiji Hishimuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Nariyasu Mano
- Faculty of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Masaki Matsuura
- Faculty of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Yuji Sato
- Faculty of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Masateru Nakasone
- Faculty of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Yohei Honkura
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jun Suzuki
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukio Katori
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masaharu Nakayama
- Department of Medical Informatics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
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3
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Sakurai-Yageta M, Kumada K, Gocho C, Makino S, Uruno A, Tadaka S, Motoike IN, Kimura M, Ito S, Otsuki A, Narita A, Kudo H, Aoki Y, Danjoh I, Yasuda J, Kawame H, Minegishi N, Koshiba S, Fuse N, Tamiya G, Yamamoto M, Kinoshita K. Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs. J Biochem 2021; 170:399-410. [PMID: 34131746 PMCID: PMC8510329 DOI: 10.1093/jb/mvab060] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/27/2021] [Indexed: 01/12/2023] Open
Abstract
Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In the Tohoku Medical Megabank Project, we have been developing a series of Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Here, we designed a novel version of the SNP array for the Japanese population, called Japonica Array NEO (JPA NEO), comprising a total of 666,883 markers. Among them, 654,246 tag SNPs of autosomes and X chromosome were selected from an expanded reference panel of 3,552 Japanese, 3.5KJPNv2, using pairwise r2 of linkage disequilibrium measures. Additionally, 28,298 markers were included for the evaluation of previously identified disease risk markers from the literature and databases, and those present in the Japanese population were extracted using the reference panel. Through genotyping 286 Japanese samples, we found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5–5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. From these results, JPA NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores.
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Affiliation(s)
- Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Chinatsu Gocho
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Satoshi Makino
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Masae Kimura
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Shin Ito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Hisaaki Kudo
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
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4
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Saito S, Aoki Y, Tamahara T, Goto M, Matsui H, Kawashima J, Danjoh I, Hozawa A, Kuriyama S, Suzuki Y, Fuse N, Kure S, Yamashita R, Tanabe O, Minegishi N, Kinoshita K, Tsuboi A, Shimizu R, Yamamoto M. Oral Microbiome Analysis in Prospective Genome Cohort Studies of the Tohoku Medical Megabank Project. Front Cell Infect Microbiol 2021; 10:604596. [PMID: 33585276 PMCID: PMC7878372 DOI: 10.3389/fcimb.2020.604596] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/07/2020] [Indexed: 12/26/2022] Open
Abstract
A baseline oral microbiome study of the Tohoku Medical Megabank Organization (TMM) was planned to characterize the profile of the oral microbiome in the Japanese population. The study also aimed to clarify risk factors for multifactorial diseases by integrated analysis of the oral microbiome and host genome/omics information. From 2013 to 2016, we collected three types of oral biospecimens, saliva, supragingival plaque, and tongue swab, from a total of 25,101 participants who had a dental examination in TMM. In this study, we used two independent cohorts; the Community-Based Cohort and Birth and Three-Generation Cohort as discovery and validation cohorts, respectively, and we selected participants examined by a single dentist. We found through the 16S ribosomal RNA gene sequencing analysis of 834 participants of the Community-Based Cohort Study that there are differences in the microbial composition and community structure between saliva and plaque. The species diversities in both saliva and plaque were increased in correlation with the severity of periodontal disease. These results were nicely reproduced in the analysis of 455 participants of the Birth and Three-Generation Cohort Study. In addition, strong positive and negative associations of microbial taxa in both plaque and saliva with periodontitis-associated biofilm formation were detected by co-occurrence network analysis. The classes Actinobacteria and Bacilli, including oral health-associated bacterial species, showed a positive correlation in saliva. These results revealed differences in microbial composition and community structure between saliva and plaque and a correlation between microbial species and the severity of periodontal disease. We expect that the large database of the oral microbiome in the TMM biobank will help in the discovery of novel targets for the treatment and prevention of oral diseases, as well as for the discovery of therapeutic and/or preventive targets of systemic diseases.
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Affiliation(s)
- Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Toru Tamahara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Maki Goto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroyuki Matsui
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Clinical Genetics, Ageo Central General Hospital, Ageo, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Riu Yamashita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Biosample Research Center, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
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5
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Nakayama A, Nakatochi M, Kawamura Y, Yamamoto K, Nakaoka H, Shimizu S, Higashino T, Koyama T, Hishida A, Kuriki K, Watanabe M, Shimizu T, Ooyama K, Ooyama H, Nagase M, Hidaka Y, Matsui D, Tamura T, Nishiyama T, Shimanoe C, Katsuura-Kamano S, Takashima N, Shirai Y, Kawaguchi M, Takao M, Sugiyama R, Takada Y, Nakamura T, Nakashima H, Tsunoda M, Danjoh I, Hozawa A, Hosomichi K, Toyoda Y, Kubota Y, Takada T, Suzuki H, Stiburkova B, Major TJ, Merriman TR, Kuriyama N, Mikami H, Takezaki T, Matsuo K, Suzuki S, Hosoya T, Kamatani Y, Kubo M, Ichida K, Wakai K, Inoue I, Okada Y, Shinomiya N, Matsuo H. Subtype-specific gout susceptibility loci and enrichment of selection pressure on ABCG2 and ALDH2 identified by subtype genome-wide meta-analyses of clinically defined gout patients. Ann Rheum Dis 2020; 79:657-665. [PMID: 32238385 PMCID: PMC7213308 DOI: 10.1136/annrheumdis-2019-216644] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 01/01/2023]
Abstract
Objectives Genome-wide meta-analyses of clinically defined gout were performed to identify subtype-specific susceptibility loci. Evaluation using selection pressure analysis with these loci was also conducted to investigate genetic risks characteristic of the Japanese population over the last 2000–3000 years. Methods Two genome-wide association studies (GWASs) of 3053 clinically defined gout cases and 4554 controls from Japanese males were performed using the Japonica Array and Illumina Array platforms. About 7.2 million single-nucleotide polymorphisms were meta-analysed after imputation. Patients were then divided into four clinical subtypes (the renal underexcretion type, renal overload type, combined type and normal type), and meta-analyses were conducted in the same manner. Selection pressure analyses using singleton density score were also performed on each subtype. Results In addition to the eight loci we reported previously, two novel loci, PIBF1 and ACSM2B, were identified at a genome-wide significance level (p<5.0×10–8) from a GWAS meta-analysis of all gout patients, and other two novel intergenic loci, CD2-PTGFRN and SLC28A3-NTRK2, from normal type gout patients. Subtype-dependent patterns of Manhattan plots were observed with subtype GWASs of gout patients, indicating that these subtype-specific loci suggest differences in pathophysiology along patients’ gout subtypes. Selection pressure analysis revealed significant enrichment of selection pressure on ABCG2 in addition to ALDH2 loci for all subtypes except for normal type gout. Conclusions Our findings on subtype GWAS meta-analyses and selection pressure analysis of gout will assist elucidation of the subtype-dependent molecular targets and evolutionary involvement among genotype, phenotype and subtype-specific tailor-made medicine/prevention of gout and hyperuricaemia.
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Affiliation(s)
- Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Medical Squadron, Air Base Group, Western Aircraft Control and Warning Wing, Japan Air Self-Defense Force, Kasuga, Japan
| | - Masahiro Nakatochi
- Division of Department of Nursing, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of General Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Ken Yamamoto
- Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Teruhide Koyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kiyonori Kuriki
- Laboratory of Public Health, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Miki Watanabe
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Toru Shimizu
- Midorigaoka Hospital, Takatsuki, Japan.,Kyoto Industrial Health Association, Kyoto, Japan
| | | | | | | | | | - Daisuke Matsui
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takashi Tamura
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takeshi Nishiyama
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Chisato Shimanoe
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan.,Clinical Research Center, Saga University Hospital, Saga, Japan
| | - Sakurako Katsuura-Kamano
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Naoyuki Takashima
- Department of Health Science, Shiga University of Medical Science, Otsu, Japan.,Department of Public Health, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of Urology, National Defense Medical College, Tokorozawa, Japan
| | - Mikiya Takao
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan.,Department of Surgery, National Defense Medical College, Tokorozawa, Japan
| | - Ryo Sugiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Yuzo Takada
- Faculty of Medical Science, Teikyo University of Science, Tokyo, Japan
| | - Takahiro Nakamura
- Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Masashi Tsunoda
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Japan
| | - Inaho Danjoh
- Group of Privacy Controls, Tohoku Medical Megabank Organization, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yu Toyoda
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Yu Kubota
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Blanka Stiburkova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Institute of Rheumatology, Prague, Czech Republic
| | - Tanya J Major
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Nagato Kuriyama
- Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Toshiro Takezaki
- Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School Medical Science, Nagoya, Japan
| | - Tatsuo Hosoya
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kimiyoshi Ichida
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology, Tokyo University of Pharmacy and Life Science, Hachioji, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Japan
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6
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Fuse N, Sakurai-Yageta M, Katsuoka F, Danjoh I, Shimizu R, Tamiya G, Nagami F, Kawame H, Higuchi S, Kinoshita K, Kure S, Yamamoto M. Establishment of Integrated Biobank for Precision Medicine and Personalized Healthcare: The Tohoku Medical Megabank Project. JMA J 2019; 2:113-122. [PMID: 33615021 PMCID: PMC7889718 DOI: 10.31662/jmaj.2019-0014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
The Tohoku Medical Megabank (TMM) project was established to provide creative reconstruction of the Tohoku area that suffered from a huge earthquake and ensuing tsunami (the Great East Japan Earthquake, GEJE). TMM aims to establish two large-scale genome cohorts and an integrated biobank managing biospecimen and related information. It supports community medicine by establishing next-generation medical systems through a combination of the prospective genome cohort studies with a total of 150,000 participants and genomic medicine. The strategies for genome analyses in TMM are to develop an elaborate genome reference panel by means of high-fidelity Japanese whole-genome sequence, to design custom single nucleotide polymorphism (SNP) arrays based on the reference panel, and to obtain genotype data for all the TMM cohort participants subsequently. Disease-associated genomic information and omics data, including metabolomics and microbiome analysis, provide an essential platform for precision medicine and personalized healthcare (PHC). Ethical, legal, and social issues (ELSI) and education are important for implementing genomic medicine. The major considerations of ELSI regarding each participant of the cohort studies are the respect for the autonomy and the protection of privacies. Moreover, developing and provide human resources not only for the TMM project but also for the social implementation of precision medicine and PHC is required. We started a pilot study of the return of genomic results for familial hypercholesterolemia (FH) as a target disease. TMM aims to establish solid platforms that support precision medicine and PHC based on the genomic and omics information and environmental and lifestyle factors of the individuals, which is one of the most advanced medical care beyond the evidenced-based medicine in the near future.
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Affiliation(s)
- Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Mika Sakurai-Yageta
- Department of Education and Training, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ritsuko Shimizu
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Molecular Hematology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Fuji Nagami
- Department of Public Relations and Planning, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroshi Kawame
- Department of Education and Training, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Higuchi
- Department of Public Relations and Planning, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Pediatrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Sendai, Japan
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7
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Sakurai-Yageta M, Kawame H, Kuriyama S, Hozawa A, Nakaya N, Nagami F, Minegishi N, Ogishima S, Takai-Igarashi T, Danjoh I, Obara T, Ishikuro M, Kobayashi T, Aizawa Y, Ishihara R, Yamamoto M, Suzuki Y. A training and education program for genome medical research coordinators in the genome cohort study of the Tohoku Medical Megabank Organization. BMC Med Educ 2019; 19:297. [PMID: 31375111 PMCID: PMC6679441 DOI: 10.1186/s12909-019-1725-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Genome cohort studies are used to analyze interactions between genetic and environmental factors, providing valuable information for personalized healthcare. Large-scale and long-term cohort studies require a number of specially trained personnel, of whom those involved in obtaining informed consent play a vital role, especially during the initial phase of such studies. The Japanese Society of Human Genetics (JSHG) previously established a certification system for genome medical research coordinators (GMRCs) responsible for obtaining written consent via face-to-face explanation. Meanwhile, in the Tohoku Medical Megabank Organization (ToMMo), GMRCs are expected to play important roles not only in obtaining informed consent and conducting various assessments, but also in communicating with participants throughout the long-term follow-up. Based on the JSHG program, we therefore developed a specific education and training program for ToMMo GMRCs consisting of 17 lectures, one practical training session on the informed consent procedure, and written and interview examinations. Re-education workshops aimed at self-improvement are also carried out following certification. In this study, we evaluated the education and training program in terms of overall understanding, usefulness, and satisfaction using an anonymous questionnaire. METHODS An anonymous questionnaire addressing each aspect of the education and training program (understanding, usefulness, and satisfaction) was distributed among 152 qualified ToMMo GMRCs. Responses were received from 94 participants (61.8%). RESULTS There was a significant association between the level of overall understanding of lectures and medical qualification (nurse or clinical laboratory technologist), but not with age or educational background. The level of understanding and overall usefulness were lower in sessions related to genetics and epidemiology than those dealing with ToMMo practices. In the re-education workshops, GMRCs showed a preference for and hoped to learn more about both background knowledge and research progress in the ToMMo. CONCLUSIONS The results of our questionnaire suggest that not all ToMMo GMRCs are able to understand everything during the initial education and training program, especially in terms of genomic medicine. Continuous re-education is therefore vital in improving knowledge, skills and motivation, and preparing GMRCs for a specialist role in community-based personalized healthcare.
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Affiliation(s)
- Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
- International Research Institute of Disaster Science, 468-1 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8572 Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Yayoi Aizawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Rino Ishihara
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Ageo Central General Hospital, 1-10-10 Kashiwaza, Ageo, Saitama, 362-8588 Japan
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8
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Kiniwa Y, Yasuda J, Saito S, Saito R, Motoike IN, Danjoh I, Kinoshita K, Fuse N, Yamamoto M, Okuyama R. Identification of genetic alterations in extramammary Paget disease using whole exome analysis. J Dermatol Sci 2019; 94:229-235. [DOI: 10.1016/j.jdermsci.2019.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022]
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9
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Yasuda J, Kinoshita K, Katsuoka F, Danjoh I, Sakurai-Yageta M, Motoike IN, Kuroki Y, Saito S, Kojima K, Shirota M, Saigusa D, Otsuki A, Kawashima J, Yamaguchi-Kabata Y, Tadaka S, Aoki Y, Mimori T, Kumada K, Inoue J, Makino S, Kuriki M, Fuse N, Koshiba S, Tanabe O, Nagasaki M, Tamiya G, Shimizu R, Takai-Igarashi T, Ogishima S, Hozawa A, Kuriyama S, Sugawara J, Tsuboi A, Kiyomoto H, Ishii T, Tomita H, Minegishi N, Suzuki Y, Suzuki K, Kawame H, Tanaka H, Taki Y, Yaegashi N, Kure S, Nagami F, Kosaki K, Sutoh Y, Hachiya T, Shimizu A, Sasaki M, Yamamoto M. Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare. J Biochem 2019; 165:139-158. [PMID: 30452759 DOI: 10.1093/jb/mvy096] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/10/2018] [Indexed: 12/29/2022] Open
Abstract
Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC.
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Affiliation(s)
- Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Japan.,Institute of Development, Aging, and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Yoko Kuroki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,United Centers for Advanced Research and Translational Medicine
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Takahiro Mimori
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Satoshi Makino
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Miho Kuriki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Molecular Hematology, Tohoku University Graduate School of Medicine, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Tadashi Ishii
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Education and Support for Community Medicine, Tohoku University Graduate School of Medicine, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Hiroshi Tanaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Medical Data Science Promotion Office, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, Japan
| | - Yasuyuki Taki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Institute of Development, Aging, and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Obstetrics and Gynecology
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Pediatrics, Tohoku University Graduate School of Medicine, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | | | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Yoichi Sutoh
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center
| | - Tsuyoshi Hachiya
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center.,Division of Ultrahigh Field MRI, Institute for Biomedical Sciences Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
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10
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Yasuda J, Katsuoka F, Danjoh I, Kawai Y, Kojima K, Nagasaki M, Saito S, Yamaguchi-Kabata Y, Tadaka S, Motoike IN, Kumada K, Sakurai-Yageta M, Tanabe O, Fuse N, Tamiya G, Higasa K, Matsuda F, Yasuda N, Iwasaki M, Sasaki M, Shimizu A, Kinoshita K, Yamamoto M. Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project. BMC Genomics 2018; 19:551. [PMID: 30041597 PMCID: PMC6057088 DOI: 10.1186/s12864-018-4942-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022] Open
Abstract
Background Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify strongly associated variants in genome-wide association studies. The Tohoku Medical Megabank (TMM) project was established to support the development of precision medicine, together with the whole-genome sequencing of 1070 human genomes from individuals in the Miyagi region (Northeast Japan) and the construction of the 1070 Japanese genome reference panel (1KJPN). Here, we investigated the performance of 1KJPN for genotype imputation of Japanese samples not included in the TMM project and compared it with other population reference panels. Results We found that the 1KJPN population was more similar to other Japanese populations, Nagahama (south-central Japan) and Aki (Shikoku Island), than to East Asian populations in the 1000 Genomes Project other than JPT, suggesting that the large-scale collection (more than 1000) of Japanese genomes from the Miyagi region covered many of the genetic variations of Japanese in mainland Japan. Moreover, 1KJPN outperformed the phase 3 reference panel of the 1000 Genomes Project (1KGPp3) for Japanese samples, and IKJPN showed similar imputation rates for the TMM and other Japanese samples for SNPs with minor allele frequencies (MAFs) higher than 1%. Conclusions 1KJPN covered most of the variants found in the samples from areas of the Japanese mainland outside the Miyagi region, implying 1KJPN is representative of the Japanese population’s genomes. 1KJPN and successive reference panels are useful genome reference panels for the mainland Japanese population. Importantly, the addition of whole genome sequences not included in the 1KJPN panel improved imputation efficiencies for SNPs with MAFs under 1% for samples from most regions of the Japanese archipelago. Electronic supplementary material The online version of this article (10.1186/s12864-018-4942-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Yasuda
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan.
| | - Fumiki Katsuoka
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Inaho Danjoh
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Yosuke Kawai
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan.,Present address: Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, 113-0033, Tokyo, Japan
| | - Kaname Kojima
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Masao Nagasaki
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Sakae Saito
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Yumi Yamaguchi-Kabata
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Shu Tadaka
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Ikuko N Motoike
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Kazuki Kumada
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Mika Sakurai-Yageta
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Osamu Tanabe
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Nobuo Fuse
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Gen Tamiya
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Koichiro Higasa
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Sakyo-ku, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Sakyo-ku, Japan
| | - Nobufumi Yasuda
- Department of Public Health, Kochi University Medical School, Nankoku-shi, 783-8505, Kochi, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, 104-0045, Chuo-ku, Japan
| | - Makoto Sasaki
- Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, 028-3694, Japan.,Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Kengo Kinoshita
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan.,Graduate School of Information Sciences, Tohoku University, Aoba-ku, Sendai, 980-8579, Miyagi, Japan
| | - Masayuki Yamamoto
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan. .,Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Miyagi, Japan.
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11
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Koshiba S, Motoike I, Saigusa D, Inoue J, Shirota M, Katoh Y, Katsuoka F, Danjoh I, Hozawa A, Kuriyama S, Minegishi N, Nagasaki M, Takai-Igarashi T, Ogishima S, Fuse N, Kure S, Tamiya G, Tanabe O, Yasuda J, Kinoshita K, Yamamoto M. Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project. Genes Cells 2018; 23:406-417. [PMID: 29701317 DOI: 10.1111/gtc.12588] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/22/2018] [Indexed: 01/05/2023]
Abstract
Population-based prospective cohort studies are indispensable for modern medical research as they provide important knowledge on the influences of many kinds of genetic and environmental factors on the cause of disease. Although traditional cohort studies are mainly conducted using questionnaires and physical examinations, modern cohort studies incorporate omics and genomic approaches to obtain comprehensive physical information, including genetic information. Here, we report the design and midterm results of multi-omics analysis on population-based prospective cohort studies from the Tohoku Medical Megabank (TMM) Project. We have incorporated genomic and metabolomic studies in the TMM cohort study as both metabolome and genome analyses are suitable for high-throughput analysis of large-scale cohort samples. Moreover, an association study between the metabolome and genome show that metabolites are an important intermediate phenotype connecting genetic and lifestyle factors to physical and pathologic phenotypes. We apply our metabolome and genome analyses to large-scale cohort samples in the following studies.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ikuko Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yasutake Katoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
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12
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Nakayama A, Nakaoka H, Yamamoto K, Sakiyama M, Shaukat A, Toyoda Y, Okada Y, Kamatani Y, Nakamura T, Takada T, Inoue K, Yasujima T, Yuasa H, Shirahama Y, Nakashima H, Shimizu S, Higashino T, Kawamura Y, Ogata H, Kawaguchi M, Ohkawa Y, Danjoh I, Tokumasu A, Ooyama K, Ito T, Kondo T, Wakai K, Stiburkova B, Pavelka K, Stamp LK, Dalbeth N, Sakurai Y, Suzuki H, Hosoyamada M, Fujimori S, Yokoo T, Hosoya T, Inoue I, Takahashi A, Kubo M, Ooyama H, Shimizu T, Ichida K, Shinomiya N, Merriman TR, Matsuo H. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes. Ann Rheum Dis 2016; 76:869-877. [PMID: 27899376 PMCID: PMC5530361 DOI: 10.1136/annrheumdis-2016-209632] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 11/05/2022]
Abstract
Objective A genome-wide association study (GWAS) of gout and its subtypes was performed to identify novel gout loci, including those that are subtype-specific. Methods Putative causal association signals from a GWAS of 945 clinically defined gout cases and 1213 controls from Japanese males were replicated with 1396 cases and 1268 controls using a custom chip of 1961 single nucleotide polymorphisms (SNPs). We also first conducted GWASs of gout subtypes. Replication with Caucasian and New Zealand Polynesian samples was done to further validate the loci identified in this study. Results In addition to the five loci we reported previously, further susceptibility loci were identified at a genome-wide significance level (p<5.0×10−8): urate transporter genes (SLC22A12 and SLC17A1) and HIST1H2BF-HIST1H4E for all gout cases, and NIPAL1 and FAM35A for the renal underexcretion gout subtype. While NIPAL1 encodes a magnesium transporter, functional analysis did not detect urate transport via NIPAL1, suggesting an indirect association with urate handling. Localisation analysis in the human kidney revealed expression of NIPAL1 and FAM35A mainly in the distal tubules, which suggests the involvement of the distal nephron in urate handling in humans. Clinically ascertained male patients with gout and controls of Caucasian and Polynesian ancestries were also genotyped, and FAM35A was associated with gout in all cases. A meta-analysis of the three populations revealed FAM35A to be associated with gout at a genome-wide level of significance (pmeta=3.58×10−8). Conclusions Our findings including novel gout risk loci provide further understanding of the molecular pathogenesis of gout and lead to a novel concept for the therapeutic target of gout/hyperuricaemia.
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Affiliation(s)
- Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Masayuki Sakiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan.,Department of Dermatology, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Amara Shaukat
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Yu Toyoda
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Yukinori Okada
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Takahiro Nakamura
- Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Katsuhisa Inoue
- Department of Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tomoya Yasujima
- Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Hiroaki Yuasa
- Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Yuko Shirahama
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Toshihide Higashino
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hiraku Ogata
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Makoto Kawaguchi
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Inaho Danjoh
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | | | | | - Toshimitsu Ito
- Department of Internal Medicine, Self-Defense Forces Central Hospital, Tokyo, Japan
| | - Takaaki Kondo
- Program in Radiological and Medical Laboratory Sciences, Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Blanka Stiburkova
- First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Institute of Inherited Metabolic Disorders, Prague, Czech Republic.,Institute of Rheumatology, Prague, Czech Republic
| | | | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Grafton, Auckland, New Zealand
| | | | - Yutaka Sakurai
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Makoto Hosoyamada
- Department of Human Physiology and Pathology, Faculty of Pharma-Sciences, Teikyo University, Tokyo, Japan
| | - Shin Fujimori
- Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Takashi Yokoo
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Tatsuo Hosoya
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Omics Research Center, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan
| | | | - Toru Shimizu
- Midorigaoka Hospital, Takatsuki, Osaka, Japan.,Kyoto Industrial Health Association, Kyoto, Japan
| | - Kimiyoshi Ichida
- Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan.,Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Tony R Merriman
- Department of Biochemisty, University of Otago, Dunedin, New Zealand
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
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13
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Koshiba S, Motoike I, Kojima K, Hasegawa T, Shirota M, Saito T, Saigusa D, Danjoh I, Katsuoka F, Ogishima S, Kawai Y, Yamaguchi-Kabata Y, Sakurai M, Hirano S, Nakata J, Motohashi H, Hozawa A, Kuriyama S, Minegishi N, Nagasaki M, Takai-Igarashi T, Fuse N, Kiyomoto H, Sugawara J, Suzuki Y, Kure S, Yaegashi N, Tanabe O, Kinoshita K, Yasuda J, Yamamoto M. The structural origin of metabolic quantitative diversity. Sci Rep 2016; 6:31463. [PMID: 27528366 PMCID: PMC4985752 DOI: 10.1038/srep31463] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/18/2016] [Indexed: 12/21/2022] Open
Abstract
Relationship between structural variants of enzymes and metabolic phenotypes in human population was investigated based on the association study of metabolite quantitative traits with whole genome sequence data for 512 individuals from a population cohort. We identified five significant associations between metabolites and non-synonymous variants. Four of these non-synonymous variants are located in enzymes involved in metabolic disorders, and structural analyses of these moderate non-synonymous variants demonstrate that they are located in peripheral regions of the catalytic sites or related regulatory domains. In contrast, two individuals with larger changes of metabolite levels were also identified, and these individuals retained rare variants, which caused non-synonymous variants located near the catalytic site. These results are the first demonstrations that variant frequency, structural location, and effect for phenotype correlate with each other in human population, and imply that metabolic individuality and susceptibility for diseases may be elicited from the moderate variants and much more deleterious but rare variants.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Ikuko Motoike
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan
| | - Kaname Kojima
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Takanori Hasegawa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Tomo Saito
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Miyuki Sakurai
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sachiko Hirano
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junichi Nakata
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hozumi Motohashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Shigeo Kure
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Jun Yasuda
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
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14
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Pan X, Nariai N, Fukuhara N, Saito S, Sato Y, Katsuoka F, Kojima K, Kuroki Y, Danjoh I, Saito R, Hasegawa S, Okitsu Y, Kondo A, Onishi Y, Nagami F, Kiyomoto H, Hozawa A, Fuse N, Nagasaki M, Shimizu R, Yasuda J, Harigae H, Yamamoto M. Monitoring of minimal residual disease in early T-cell precursor acute lymphoblastic leukaemia by next-generation sequencing. Br J Haematol 2016; 176:318-321. [PMID: 26822323 DOI: 10.1111/bjh.13948] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaoqing Pan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoki Nariai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Noriko Fukuhara
- Department of Haematology and Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Sakae Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yukuto Sato
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoko Kuroki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Rumiko Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shin Hasegawa
- Department of Haematology and Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Yoko Okitsu
- Department of Haematology and Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Aiko Kondo
- Department of Haematology and Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Yasushi Onishi
- Department of Haematology and Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Fuji Nagami
- Department of Public Relations and Planning, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hideyasu Kiyomoto
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ritsuko Shimizu
- Department of Molecular Haematology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jun Yasuda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hideo Harigae
- Department of Haematology and Rheumatology, Tohoku University Hospital, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
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15
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Nagasaki M, Yasuda J, Katsuoka F, Nariai N, Kojima K, Kawai Y, Yamaguchi-Kabata Y, Yokozawa J, Danjoh I, Saito S, Sato Y, Mimori T, Tsuda K, Saito R, Pan X, Nishikawa S, Ito S, Kuroki Y, Tanabe O, Fuse N, Kuriyama S, Kiyomoto H, Hozawa A, Minegishi N, Douglas Engel J, Kinoshita K, Kure S, Yaegashi N, Yamamoto M. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nat Commun 2015; 6:8018. [PMID: 26292667 PMCID: PMC4560751 DOI: 10.1038/ncomms9018] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 07/07/2015] [Indexed: 12/19/2022] Open
Abstract
The Tohoku Medical Megabank Organization reports the whole-genome sequences of 1,070 healthy Japanese individuals and construction of a Japanese population reference panel (1KJPN). Here we identify through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. We also catalogue structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies. The Tohoku Medical Megabank Organization establishes a biobank with detailed patient health care and genome information. Here the authors analyse whole-genome sequences of 1,070 Japanese individuals, allowing them to catalogue 21 million single-nucleotide variants including 12 million novel ones.
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Affiliation(s)
- Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Naoki Nariai
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Junji Yokozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Yukuto Sato
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Takahiro Mimori
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Kaoru Tsuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Rumiko Saito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Xiaoqing Pan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Satoshi Nishikawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Shin Ito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Yoko Kuroki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.,International Research Institute of Disaster Science, Tohoku University, 468-1, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109-2200, USA
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | | | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
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16
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Yamada T, Abei M, Danjoh I, Shirota R, Yamashita T, Endo S, Hyodo I, Nakamura Y. Abstract 1397: Identification of a hepatocellular carcinoma cell line capable of monitoring the differentiation of CD13(+)CD166(-) cancer stem cells and effects of sorafenib. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Recent cancer stem cell (CSC) research has highlighted the necessity to develop drugs targeting CSCs. However, only few in vitro models are available which show CSC hierarchy and allow monitoring of CSC differentiation and screening of drugs targeting CSC.
Aim: In the present study, we aimed to identify such hepatocellular carcinoma (HCC) cell line(s).
Methods: Based on a hypothesis that the proportion of CSCs would decrease during culture because of their differentiation into progenitors (population switch), we tested the positivity of several markers (CD13, EpCAM, CD133, CD44, CD90, CD24, CD166) in HCC cell lines (HuH-7, Li-7, PLC/PRF/5, HLF, HLE) before and after 2 months culture.
Results: Only Li-7 cells showed relevant population switch: the proportion of CD13 decreased, while that of CD166 increased during the culture. High tumorigenicity of Li-7 was lost after the population switch. CD13(+)/CD166(-) cells showed slow growth and reconstructed the bulk Li-7 populations composed of CD13(+)/CD166(-), CD13(-)/CD166(-) and CD13(-)/CD166(+) fractions, while CD13(-)/CD166(+) cells showed rapid growth but could not reproduce any other cell populations. CD13(+)/CD166(-) cells showed high ALDH activity, spheroid forming ability and resistance to 5FU. Microarray analysis demonstrated higher expression of stemness-related genes in CD166(-) than CD166(+) fraction. These results indicated the hierarchy of Li-7 cells, in which CD13(+)/CD166(-) and CD13(-)/CD166(+) cells serve as slow growing CSCs and rapid growing progenitors, respectively. Interestingly, sorafenib selectively targeted CD166(-) fraction including CD13(+) CSCs, which exhibited higher mRNA expression of FGF3 and FGF4, candidate biomarkers for sorafenib. 5-FU followed by sorafenib inhibited the growth of bulk Li-7 cells more effectively than reverse sequence or either alone.
Conclusions: We identified an useful cell line Li-7 capable of monitoring the CD13 (+) CSC differentiation and screening the drugs targeting the CSCs of HCC and found that sorafenib preferentially targeted CD13(+) CSCs in vitro. Screening cell lines for “population switch” may be useful to identify novel candidate model systems for screening drugs targeting CSCs.
Citation Format: Takeshi Yamada, Masato Abei, Inaho Danjoh, Ryoko Shirota, Taro Yamashita, Shinji Endo, Ichinosuke Hyodo, Yukio Nakamura. Identification of a hepatocellular carcinoma cell line capable of monitoring the differentiation of CD13(+)CD166(-) cancer stem cells and effects of sorafenib. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1397. doi:10.1158/1538-7445.AM2015-1397
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Affiliation(s)
- Takeshi Yamada
- 1Dept. of Gastroenterology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masato Abei
- 1Dept. of Gastroenterology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Inaho Danjoh
- 2Functional Evaluation of Genomic Polymorphisms, Tohoku Medical Megabank Organization, Sendai, Miyagi, Japan
| | - Ryoko Shirota
- 3Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Taro Yamashita
- 4Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Ishikawa, Japan
| | - Shinji Endo
- 1Dept. of Gastroenterology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Ichinosuke Hyodo
- 1Dept. of Gastroenterology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yukio Nakamura
- 3Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
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Yamada T, Abei M, Danjoh I, Shirota R, Yamashita T, Hyodo I, Nakamura Y. Identification of a unique hepatocellular carcinoma line, Li-7, with CD13(+) cancer stem cells hierarchy and population change upon its differentiation during culture and effects of sorafenib. BMC Cancer 2015; 15:260. [PMID: 25885470 PMCID: PMC4396571 DOI: 10.1186/s12885-015-1297-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 03/31/2015] [Indexed: 12/26/2022] Open
Abstract
Backgrounds Cancer stem cell (CSC) research has highlighted the necessity of developing drugs targeting CSCs. We investigated a hepatocellular carcinoma (HCC) cell line that not only has CSC hierarchy but also shows phenotypic changes (population changes) upon differentiation of CSC during culture and can be used for screening drugs targeting CSC. Methods Based on a hypothesis that the CSC proportion should decrease upon its differentiation into progenitors (population change), we tested HCC cell lines (HuH-7, Li-7, PLC/PRF/5, HLF, HLE) before and after 2 months culture for several markers (CD13, EpCAM, CD133, CD44, CD90, CD24, CD166). Tumorigenicity was tested using nude mice. To evaluate the CSC hierarchy, we investigated reconstructivity, proliferation, ALDH activity, spheroid formation, chemosensitivity and microarray analysis of the cell populations sorted by FACS. Results Only Li-7 cells showed a population change during culture: the proportion of CD13 positive cells decreased, while that of CD166 positive cells increased. The high tumorigenicity of the Li-7 was lost after the population change. CD13(+)/CD166(−) cells showed slow growth and reconstructed the bulk Li-7 populations composed of CD13(+)/CD166(−), CD13(−)/CD166(−) and CD13(−)/CD166(+) fractions, whereas CD13(−)/CD166(+) cells showed rapid growth but could not reproduce any other population. CD13(+)/CD166(−) cells showed high ALDH activity, spheroid forming ability and resistance to 5-fluorouracil. Microarray analysis demonstrated higher expression of stemness-related genes in CD166(−) than CD166(+) fraction. These results indicated a hierarchy in Li-7 cells, in which CD13(+)/CD166(−) and CD13(−)/CD166(+) cells serve as slow growing CSCs and rapid growing progenitors, respectively. Sorafenib selectively targeted the CD166(−) fraction, including CD13(+) CSCs, which exhibited higher mRNA expression for FGF3 and FGF4, candidate biomarkers for sorafenib. 5-fluorouracil followed by sorafenib inhibited the growth of bulk Li-7 cells more effectively than the reverse sequence or either alone. Conclusions We identified a unique HCC line, Li-7, which not only shows heterogeneity for a CD13(+) CSC hierarchy, but also undergoes a “population change” upon CSC differentiation. Sorafenib targeted the CSC in vitro, supporting the use of this model for screening drugs targeting the CSC. This type of “heterogeneous, unstable” cell line may prove more useful in the CSC era than conventional “homogeneous, stable” cell lines. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1297-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takeshi Yamada
- Division of Gastroenterology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8575, Japan. .,Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Masato Abei
- Division of Gastroenterology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Inaho Danjoh
- Functional Evaluation of Genomic Polymorphisms, Tohoku Medical Megabank Organization, Sendai, Japan.
| | - Ryoko Shirota
- Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
| | - Taro Yamashita
- Department of Gastroenterology, Kanazawa University Hospital, 13-1, Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.
| | - Ichinosuke Hyodo
- Division of Gastroenterology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8575, Japan.
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan.
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Matsuo H, Yamamoto K, Nakaoka H, Nakayama A, Sakiyama M, Chiba T, Takahashi A, Nakamura T, Nakashima H, Takada Y, Danjoh I, Shimizu S, Abe J, Kawamura Y, Terashige S, Ogata H, Tatsukawa S, Yin G, Okada R, Morita E, Naito M, Tokumasu A, Onoue H, Iwaya K, Ito T, Takada T, Inoue K, Kato Y, Nakamura Y, Sakurai Y, Suzuki H, Kanai Y, Hosoya T, Hamajima N, Inoue I, Kubo M, Ichida K, Ooyama H, Shimizu T, Shinomiya N. Genome-wide association study of clinically defined gout identifies multiple risk loci and its association with clinical subtypes. Ann Rheum Dis 2015; 75:652-9. [PMID: 25646370 PMCID: PMC4819613 DOI: 10.1136/annrheumdis-2014-206191] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 01/06/2015] [Indexed: 01/28/2023]
Abstract
OBJECTIVE Gout, caused by hyperuricaemia, is a multifactorial disease. Although genome-wide association studies (GWASs) of gout have been reported, they included self-reported gout cases in which clinical information was insufficient. Therefore, the relationship between genetic variation and clinical subtypes of gout remains unclear. Here, we first performed a GWAS of clinically defined gout cases only. METHODS A GWAS was conducted with 945 patients with clinically defined gout and 1213 controls in a Japanese male population, followed by replication study of 1048 clinically defined cases and 1334 controls. RESULTS Five gout susceptibility loci were identified at the genome-wide significance level (p<5.0×10(-8)), which contained well-known urate transporter genes (ABCG2 and SLC2A9) and additional genes: rs1260326 (p=1.9×10(-12); OR=1.36) of GCKR (a gene for glucose and lipid metabolism), rs2188380 (p=1.6×10(-23); OR=1.75) of MYL2-CUX2 (genes associated with cholesterol and diabetes mellitus) and rs4073582 (p=6.4×10(-9); OR=1.66) of CNIH-2 (a gene for regulation of glutamate signalling). The latter two are identified as novel gout loci. Furthermore, among the identified single-nucleotide polymorphisms (SNPs), we demonstrated that the SNPs of ABCG2 and SLC2A9 were differentially associated with types of gout and clinical parameters underlying specific subtypes (renal underexcretion type and renal overload type). The effect of the risk allele of each SNP on clinical parameters showed significant linear relationships with the ratio of the case-control ORs for two distinct types of gout (r=0.96 [p=4.8×10(-4)] for urate clearance and r=0.96 [p=5.0×10(-4)] for urinary urate excretion). CONCLUSIONS Our findings provide clues to better understand the pathogenesis of gout and will be useful for development of companion diagnostics.
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Affiliation(s)
- Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan Medical Group, Headquarters, Iwo-to Air Base Group, Japan Air Self-Defense Force, Tokyo, Japan
| | - Masayuki Sakiyama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan Department of Dermatology, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Toshinori Chiba
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan
| | - Takahiro Nakamura
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan Laboratory for Mathematics, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hiroshi Nakashima
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yuzo Takada
- The Central Research Institute, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Inaho Danjoh
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Seiko Shimizu
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Junko Abe
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Yusuke Kawamura
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Sho Terashige
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hiraku Ogata
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Seishiro Tatsukawa
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Guang Yin
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan Department of Nutritional Sciences, Faculty of Health and Welfare, Seinan Jo Gakuin University, Fukuoka, Japan
| | - Rieko Okada
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Emi Morita
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | | | - Hiroyuki Onoue
- Department of Internal Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Keiichi Iwaya
- Department of Pathology, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Toshimitsu Ito
- Department of Internal Medicine, Self-Defense Forces Central Hospital, Tokyo, Japan
| | - Tappei Takada
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Katsuhisa Inoue
- Department of Biopharmaceutics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Yukio Kato
- Faculty of Pharmacy, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Yutaka Sakurai
- Department of Preventive Medicine and Public Health, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Tokyo, Japan
| | - Yoshikatsu Kanai
- Division of Bio-system Pharmacology, Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tatsuo Hosoya
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan Department of Pathophysiology and Therapy in Chronic Kidney Disease, Jikei University School of Medicine, Tokyo, Japan
| | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa, Japan
| | - Kimiyoshi Ichida
- Division of Kidney and Hypertension, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | | | | | - Nariyoshi Shinomiya
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
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Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, Kojima K, Nariai N, Sato Y, Yamaguchi-Kabata Y, Ito S, Kudo H, Nishijima I, Nishikawa S, Pan X, Saito R, Saito S, Saito T, Shirota M, Tsuda K, Yokozawa J, Igarashi K, Minegishi N, Tanabe O, Fuse N, Nagasaki M, Kinoshita K, Yasuda J, Yamamoto M. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population. BMC Genomics 2014; 15:673. [PMID: 25109789 PMCID: PMC4138778 DOI: 10.1186/1471-2164-15-673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 08/01/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. RESULTS Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. CONCLUSIONS Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.
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Affiliation(s)
- Ikuko N Motoike
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Mitsuyo Matsumoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Fumiki Katsuoka
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaname Kojima
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Naoki Nariai
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yukuto Sato
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yumi Yamaguchi-Kabata
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Shin Ito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hisaaki Kudo
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Ichiko Nishijima
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Satoshi Nishikawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Xiaoqing Pan
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Rumiko Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sakae Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Tomo Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Matsuyuki Shirota
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaoru Tsuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junji Yokozawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kazuhiko Igarashi
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Osamu Tanabe
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Nobuo Fuse
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masao Nagasaki
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kengo Kinoshita
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, Sendai, 980-8575 Japan
| | - Jun Yasuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masayuki Yamamoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
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Danjoh I, Shirota R, Hiroyama T, Nakamura Y. Dominant expansion of a cryptic subclone with an abnormal karyotype in B lymphoblastoid cell lines during culture. Cytogenet Genome Res 2012; 139:88-96. [PMID: 23128794 DOI: 10.1159/000343757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2012] [Indexed: 11/19/2022] Open
Abstract
Although B lymphoblastoid cell lines (B-LCLs) are thought to maintain their original genomic structures during long-term culture, there has been considerable disagreement on the actual genomic stability of these cells. This study was initiated to determine whether B-LCLs develop cell populations with abnormal genomes during culture and to search for factors important to the maintenance of the original genome. We established continuous cultures of B-LCLs for more than 6 months and analyzed the cells using array-based comparative genome hybridization (CGH) analysis, conventional karyotyping and analysis of V(D)J recombination in the immunoglobulin (Ig) gene. We found that one B-LCL acquired an extra chromosome 4 without any other genomic rearrangements at passage 16 of continuous culture. At the Ig light- and heavy-chain loci, analysis of the major cell population showed a difference between cultures at early and later passages. Another aneuploid line was detected among B-LCLs established elsewhere and deposited previously into the RIKEN Cell Bank. Our findings indicate that some of the genomic rearrangements in B-LCLs are not caused by gradual accumulation of mutations and rearrangements during the B-LCL establishment processes, but rather as a result of a change in the cell population from clones with a normal genome to clones with de novo rearrangements. It is therefore feasible to maintain B-LCLs with a normal genomic structure by cell cloning or similar treatment.
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Affiliation(s)
- I Danjoh
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Japan
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Yamamoto T, Gomyoda T, Ito T, Saijo K, Danjoh I, Nakamura Y. Family selection study among DNA samples collected from Amerindian ethnic group (Wayuu) in northern Colombia. Forensic Science International: Genetics Supplement Series 2011. [DOI: 10.1016/j.fsigss.2011.08.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Danjoh I, Saijo K, Hiroyama T, Nakamura Y. The Sonoda-Tajima Cell Collection: a human genetics research resource with emphasis on South American indigenous populations. Genome Biol Evol 2011; 3:272-83. [PMID: 21383383 PMCID: PMC3070430 DOI: 10.1093/gbe/evr014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Sonoda–Tajima Cell Collection includes cell samples obtained from a range of ethnic minority groups across the world but in particular from South America. The collection is made all the more valuable by the fact that some of these ethnic populations have since died out, and thus it will be impossible to prepare a similar cell collection again. The collection was donated to our institute, a public cell bank in Japan, by Drs Sonoda and Tajima to make it available to researchers throughout the world. The original cell collection was composed of cryopreserved peripheral blood samples that would obviously have been rapidly exhausted if used directly. We, therefore, immortalized some samples with the Epstein–Barr virus and established B-lymphoblastoid cell lines (B-LCLs). As there is continuing controversy over whether the B-LCL genome is stably maintained, we performed an array comparative genomic hybridization (CGH) analysis to confirm the genomic stability of the cell lines. The array CGH analysis of the B-LCL lines and their parental B cells demonstrated that genomic stability was maintained in the long-term cell cultures. The B-LCLs of the Sonoda–Tajima Collection will therefore be made available to interested scientists around the world. At present, 512 B-LCLs have been developed, and we are willing to increase the number if there is sufficient demand.
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Affiliation(s)
- Inaho Danjoh
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
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Danjoh I, Sone H, Noda N, Iimura E, Nagayoshi M, Saijo K, Hiroyama T, Nakamura Y. Is parainfluenza virus a threatening virus for human cancer cell lines? Hum Cell 2009; 22:81-4. [PMID: 19624309 DOI: 10.1111/j.1749-0774.2009.00071.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Immortalized cell lines, such as human cancer cell lines, are an indispensable experimental resource for many types of biological and medical research. However, unless the cell line has been authenticated prior to use, interpretation of experimental results may be problematic. The potential problems this may cause are illustrated by studies in which authentication of cell lines has not been carried out. For example, immortalized cell lines may unknowingly be infected with viruses that alter their characteristics. In fact, parainfluenza virus type 5 (PIV5) poses a threat to the use of immortalized cell lines in biological and medical research; PIV5 infection significantly alters cellular physiology associated with the response to interferon. If PIV5 infection is widespread in immortalized cell lines, then a very large number of published studies might have to be re-evaluated. Fortunately, analyses of a large number of immortalized cell lines indicate that PIV5 infection is not widespread.
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Tsuyama N, Danjoh I, Otsuyama KI, Obata M, Tahara H, Ohta T, Ishikawa H. IL-6-induced Bcl6 variant 2 supports IL-6-dependent myeloma cell proliferation and survival through STAT3. Biochem Biophys Res Commun 2005; 337:201-8. [PMID: 16188230 DOI: 10.1016/j.bbrc.2005.09.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
IL-6 is a growth and survival factor for myeloma cells, although the mechanism by which it induces myeloma cell proliferation through gene expression is largely unknown. Microarray analysis showed that some B-cell lymphoma-associated oncogenes such as Bcl6, which is absent in normal plasma cells, were upregulated by IL-6 in IL-6-dependent myeloma cell lines. We found that Bcl6 variant 2 was upregulated by STAT3. ChIP assay and EMSA showed that STAT3 bound to the upstream region of variant 2 DNA. Expression of p53, a direct target gene of Bcl6, was downregulated in the IL-6-stimulated cells, and this process was impaired by an HDAC inhibitor. Bcl6 was knocked down by introducing small hairpin RNA, resulting in decreased proliferation and increased sensitivity to a DNA damaging agent. Thus, STAT3-inducible Bcl6 variant 2 appears to generate an important IL-6 signal that supports proliferation and survival of IL-6-dependent myeloma cells.
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Affiliation(s)
- Naohiro Tsuyama
- Department of Bio-Signal Analysis, Yamaguchi University Graduate School of Medicine, Minami Kogushi 1-1-1, Ube, Yamaguchi 755-8505, Japan.
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Nishigaki M, Aoyagi K, Danjoh I, Fukaya M, Yanagihara K, Sakamoto H, Yoshida T, Sasaki H. Discovery of aberrant expression of R-RAS by cancer-linked DNA hypomethylation in gastric cancer using microarrays. Cancer Res 2005; 65:2115-24. [PMID: 15781621 DOI: 10.1158/0008-5472.can-04-3340] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although hypomethylation was the originally identified epigenetic change in cancer, it was overlooked for many years in preference to hypermethylation. Recently, gene activation by cancer-linked hypomethylation has been rediscovered. However, in gastric cancer, genome-wide screening of the activated genes has not been found. By using microarrays, we identified 1,383 gene candidates reactivated in at least one cell line of eight gastric cancer cell lines after treatment with 5-aza-2'deoxycytidine and trichostatin A. Of the 1,383 genes, 159 genes, including oncogenes ELK1, FRAT2, R-RAS, RHOB, and RHO6, were further selected as gene candidates that are silenced by DNA methylation in normal stomach mucosa but are activated by DNA demethylation in a subset of gastric cancers. Next, we showed that demethylation of specific CpG sites within the first intron of R-RAS causes activation in more than half of gastric cancers. Introduction of siRNA into R-RAS-expressing cells resulted in the disappearance of the adhered cells, suggesting that functional blocking of the R-RAS-signaling pathway has great potential for gastric cancer therapy. Our extensive gene list provides other candidates for this class of oncogene.
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Affiliation(s)
- Michiko Nishigaki
- Genetics Division, Center of Medical Genomics, and Central Animal Laboratory, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
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Mori K, Aoyagi K, Ueda T, Danjoh I, Tsubosa Y, Yanagihara K, Matsuno Y, Sasako M, Sakamoto H, Mafune KI, Kaminishi M, Yoshida T, Terada M, Sasaki H. Highly specific marker genes for detecting minimal gastric cancer cells in cytology negative peritoneal washings. Biochem Biophys Res Commun 2004; 313:931-7. [PMID: 14706632 DOI: 10.1016/j.bbrc.2003.12.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Peritoneal wash cytology plays a pivotal role in the decision for gastric cancer treatment because advanced gastric cancer often turns out incurable with peritoneal metastasis. Molecular detection of minimal cancer cells from peritoneal washings may overcome the sensitivity boundary of conventional cytology and contribute to the prediction of the disease outcome. To select marker candidates out of ten thousands of genes, we performed microarray analyses in 12 gastric cell lines and 8 peritoneal washings of early stage cases. With 40 candidates selected by the above expression profiling, RT-PCR in 16 representative peritoneal wash samples was performed to identify genes specific to cytology positive samples. The finally selected five genes, CK20, FABP1, MUC2, TFF1, and TFF2, were then evaluated for their utility as a marker for minimal residual disease in 99 peritoneal wash samples. Nested RT-PCR using the five genes showed positive results highly specific to incurable cases (91-100%). With a high specificity, the combination of these five genes succeeded in identifying 6 out of 20 (30%) additional patients with all types of early recurrence that could not be predicted by the conventional method. The six newly identified recurrences included four non-peritoneal ones, showing that RT-PCR using the five genes without a real-time quantitative PCR technique contributes to the detection of minimal residual disease.
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Affiliation(s)
- Kazuhiko Mori
- Genetics Division, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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Abstract
In fission yeast, Schizosaccharomyces pombe, deficiency of ras1 gene causes an abnormal cell shape and abolishes mating ability. However, target genes of this signaling pathway are largely unknown because of the lack of an appropriate analysis system. To overcome this problem, we have started a novel project to categorize entire genes based on their expression levels under different growth conditions. Using this strategy, we screened genes whose expression levels were affected in the presence or absence of the ras1 gene product. For this purpose, we utilized high-density arrays of clones covering the entire genome of the fission yeast, and probed with labelled cDNA derived from various strains and growth conditions. Here, we demonstrate the detection of a low-molecular-weight heat-shock protein gene, hsp16, whose expression is very likely to be regulated by a ras-mediated signaling pathway, but not by the heat-shock response.
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Affiliation(s)
- I Danjoh
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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Iha H, Takimoto M, Danjoh I, Fujiyama A. Identification and characterization of a novel trans-membrane protein gene, pdh1, from Schizosaccharomyces pombe. DNA Res 1997; 4:393-6. [PMID: 9501995 DOI: 10.1093/dnares/4.6.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We have cloned a new gene, pdh1, from genomic DNA of fission yeast Schizosaccharomyces pombe. pdh1 is actively transcribed as 1400-nucleotide mRNA in vegetatively growing cells and can code for a 226 amino acid polypeptide (pdh1p). Computational structural prediction has revealed that the pdh1p is a highly hydrophobic protein with seven transmembrane domains. The prediction has also detected a possible C-kinase phosphorylation site within the longest hydrophilic loop.
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Affiliation(s)
- H Iha
- National Institute of Genetics, Shizuoka, Japan
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Abstract
The enzyme farnesyl transferase (FTase) catalyzes the posttranslational modification of Ras and other Ras family proteins with a C15 farnesyl group. The target proteins have a consensus -CAAX motif (X, any amino acid except leucine) at the C-terminus. Since proteins that have leucine as the C-terminal amino acid X are modified with a C20 geranylgeranyl group, it is thought that the C-terminal leucine is the signal (-CAAL motif) for selection of isoprenoid molecules. Here, we report the presence of multiple FTase activities in the fission yeast Schizosaccharomyces pombe, each seeming to correspond to a particular protein known to be modified by the farnesyl group in vivo. Using enzymic activities specific to S. pombe Ras1, we found similar affinities for FTases in the wild-type (EVSTKCCVIC) and mutant Ras1 peptide, in which the C-terminal amino acid is replaced by leucine (EVSTKCCVIL). These results suggest that recognition and selection of the correct isoprenoid group by the FTases require other amino acid sequences of the target protein in addition to the C-terminal -CAAX motif.
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Affiliation(s)
- I Danjoh
- Department of Human Genetics, National Institute of Genetics, Shizuoka, Japan
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Abstract
Schizosaccharomyces pombe contains single ras oncogene homologue, ras1, that functions in the signal transduction pathway conducting the cell's mating processes. To understand the biochemical basis of yeast ras proteins, we have purified the ras1 protein and compared the major biochemical constants with those of RAS2 protein from Saccharomyces cerevisiae and mammalian ras proteins. The purified ras1 protein showed a remarkably high Kd value for GDP binding (178 nM) and for binding with ATP. In contrast, the Kd value for GTP binding and the rate of GTPase activity were 64 nM and 77 x 10(-6) s-1 at 37 degrees C, respectively; both were higher than normal p21ras protein, but at the same level as the RAS2 protein. We directly measured rate of GTP binding and GDP binding which were 3.9 x 10(-3) s-1 and 1.8 x 10(-3) s-1 at 30 degrees C, respectively. On the other hand, exchange rates between bound and free nucleotides remained almost constant throughout the tested combination of GTP and GDP, and were several-fold lower than the binding rate. These results suggest that the release of the guanine nucleotide is the rate-limiting step in the ras-GTP/GDP cycle. As a whole, the biochemical properties of the ras1 protein are close to those of the RAS2 protein, although these two proteins function differently in the signal transduction pathway in the cells.
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Affiliation(s)
- T Onozawa
- National Institute of Genetics, Shizuoka, Japan
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