Tohoku Medical Megabank Project

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Tohoku Medical Megabank Project
ToMMo building.jpg
Building of ToMMo at Tohoku Univ.
Commercial?No
Type of projectProspective cohort study
LocationSendai, Miyagi, JAPAN (ToMMo) and Shiwa-gun, Iwate, JAPAN (IMM)
Key peopleMasayuki Yamamoto (Executive Director, ToMMo) Kozo Tanno (Executive Director, IMM)
Established2012

The Tohoku Medical Megabank Project is a national project in Japan, which started in 2012. [1] The mission of the Tohoku Medical Megabank (TMM) project is to carry out a long-term health survey in the Miyagi and Iwate prefectures, which were affected by the Great East Japan Earthquake, and provide the research infrastructure for the development of personalized medicine by establishing a biobank and conducting cohort studies. [2] [3]

Contents

The TMM project is conducted by Tohoku University's Tohoku Medical Megabank Organization (ToMMo) and Iwate Medical University's Iwate Tohoku Medical Megabank Organization (IMM).

Projects

The following cohort studies and research projects are in progress or completed.

Prospective cohort studies

The study recruited over 80,000 participants, with 50,000 from Miyagi Prefecture and 30,000 from Iwate Prefecture.

The study recruited over 70,000 participants, including over 23,000 newborns and their parents, siblings, grandparents, and extended family members. [3]

The project has been collecting various specimens, including peripheral and cord blood mononuclear cells, Buffy coat, plasma, serum, urine, breast milk, and saliva. [2]

Research projects

The project provides allele frequencies of SNVs (single nucleotide variants) and short Indels (insertions/deletions) detected by short-read whole genome sequencing (WGS) analysis of 54,000 Japanese individuals, as well as allele frequencies of structural variants detected by long-read WGS analysis of 222 individuals. [7]

The project designed ethnic-specific SNP arrays optimized for the Japanese population and performed a series of GWAS analyses and polygenic predictions with the cohort samples. [8] [9]

The project constructed a reference genome for Japanese by integrating de novo assemblies of three Japanese individuals.

Timeline

2013

2014

2015

2016

2017

2018

2019

2020

2021

2022

2023

2024

References

  1. 1 2 3 4 5 6 7 Kuriyama, Shinichi; Yaegashi, Nobuo; Nagami, Fuji; Arai, Tomohiko; Kawaguchi, Yoshio; Osumi, Noriko; Sakaida, Masaki; Suzuki, Yoichi; Nakayama, Keiko; Hashizume, Hiroaki; Tamiya, Gen (2016). "The Tohoku Medical Megabank Project: Design and Mission". Journal of Epidemiology. 26 (9): 493–511. doi:10.2188/jea.JE20150268. PMC   5008970 . PMID   27374138.
  2. 1 2 3 Minegishi, Naoko; Nishijima, Ichiko; Nobukuni, Takahiro; Kudo, Hisaaki; Ishida, Noriko; Terakawa, Takahiro; Kumada, Kazuki; Yamashita, Riu; Katsuoka, Fumiki; Ogishima, Soichi; Suzuki, Kichiya (2019). "Biobank Establishment and Sample Management in the Tohoku Medical Megabank Project". The Tohoku Journal of Experimental Medicine. 248 (1): 45–55. doi: 10.1620/tjem.248.45 . PMID   31130587. S2CID   167210746.
  3. 1 2 Kuriyama, Shinichi; Metoki, Hirohito; Kikuya, Masahiro; Obara, Taku; Ishikuro, Mami; Yamanaka, Chizuru; Nagai, Masato; Matsubara, Hiroko; Kobayashi, Tomoko; Sugawara, Junichi; Tamiya, Gen (1 February 2020). "Cohort Profile: Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study): rationale, progress and perspective". International Journal of Epidemiology. 49 (1): 18–19m. doi:10.1093/ije/dyz169. ISSN   0300-5771. PMC   7124511 . PMID   31504573.
  4. ↑ Ogishima, Soichi; Nagaie, Satoshi; Mizuno, Satoshi; Ishiwata, Ryosuke; Iida, Keita; Shimokawa, Kazuro; Takai-Igarashi, Takako; Nakamura, Naoki; Nagase, Sachiko; Nakamura, Tomohiro; Tsuchiya, Naho (10 December 2021). "dbTMM: an integrated database of large-scale cohort, genome and clinical data for the Tohoku Medical Megabank Project". Human Genome Variation. 8 (1): 44. doi:10.1038/s41439-021-00175-5. ISSN   2054-345X. PMC   8660797 . PMID   34887386.
  5. ↑ Kawame, Hiroshi; Fukushima, Akimune; Fuse, Nobuo; Nagami, Fuji; Suzuki, Yoichi; Sakurai-Yageta, Mika; Yasuda, Jun; Yamaguchi-Kabata, Yumi; Kinoshita, Kengo; Ogishima, Soichi; Takai, Takako (January 2022). "The return of individual genomic results to research participants: design and pilot study of Tohoku Medical Megabank Project". Journal of Human Genetics. 67 (1): 9–17. doi:10.1038/s10038-021-00952-8. ISSN   1435-232X. PMID   34234266. S2CID   235768398.
  6. 1 2 Yasuda, Jun; Kinoshita, Kengo; Katsuoka, Fumiki; Danjoh, Inaho; Sakurai-Yageta, Mika; Motoike, Ikuko N.; Kuroki, Yoko; Saito, Sakae; Kojima, Kaname; Shirota, Matsuyuki; Saigusa, Daisuke (1 February 2019). "Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare". Journal of Biochemistry. 165 (2): 139–158. doi:10.1093/jb/mvy096. ISSN   1756-2651. PMID   30452759.
  7. ↑ "jMorp". jmorp.megabank.tohoku.ac.jp. Retrieved 12 March 2024.
  8. ↑ Sakurai-Yageta, Mika; Kumada, Kazuki; Gocho, Chinatsu; Makino, Satoshi; Uruno, Akira; Tadaka, Shu; Motoike, Ikuko N; Kimura, Masae; Ito, Shin; Otsuki, Akihito; Narita, Akira; Kudo, Hisaaki; Aoki, Yuichi; Danjoh, Inaho; Yasuda, Jun (12 October 2021). "Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs". The Journal of Biochemistry. 170 (3): 399–410. doi:10.1093/jb/mvab060. ISSN   0021-924X. PMC   8510329 . PMID   34131746.
  9. ↑ Ojima, Takafumi; Namba, Shinichi; Suzuki, Ken; Yamamoto, Kenichi; Sonehara, Kyuto; Narita, Akira; Kamatani, Yoichiro; Tamiya, Gen; Yamamoto, Masayuki; Yamauchi, Toshimasa; Kadowaki, Takashi; Okada, Yukinori (2024). "Body mass index stratification optimizes polygenic prediction of type 2 diabetes in cross-biobank analyses" . Nature Genetics. 56 (6): 1100–1109. doi:10.1038/s41588-024-01782-y.
  10. 1 2 Takayama, Jun; Tadaka, Shu; Yano, Kenji; Katsuoka, Fumiki; Gocho, Chinatsu; Funayama, Takamitsu; Makino, Satoshi; Okamura, Yasunobu; Kikuchi, Atsuo; Sugimoto, Sachiyo; Kawashima, Junko (11 January 2021). "Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference". Nature Communications. 12 (1): 226. Bibcode:2021NatCo..12..226T. doi:10.1038/s41467-020-20146-8. ISSN   2041-1723. PMC   7801658 . PMID   33431880.
  11. 1 2 Koshiba, Seizo; Motoike, Ikuko; Saigusa, Daisuke; Inoue, Jin; Shirota, Matsuyuki; Katoh, Yasutake; Katsuoka, Fumiki; Danjoh, Inaho; Hozawa, Atsushi; Kuriyama, Shinichi; Minegishi, Naoko (June 2018). "Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project". Genes to Cells: Devoted to Molecular & Cellular Mechanisms. 23 (6): 406–417. doi: 10.1111/gtc.12588 . ISSN   1365-2443. PMID   29701317. S2CID   21700516.
  12. 1 2 Furukawa, Ryohei; Hachiya, Tsuyoshi; Ohmomo, Hideki; Shiwa, Yuh; Ono, Kanako; Suzuki, Sadafumi; Satoh, Mamoru; Hitomi, Jiro; Sobue, Kenji; Shimizu, Atsushi (19 May 2016). "Intraindividual dynamics of transcriptome and genome-wide stability of DNA methylation". Scientific Reports. 6 26424. Bibcode:2016NatSR...626424F. doi:10.1038/srep26424. ISSN   2045-2322. PMC   4872231 . PMID   27192970.
  13. ↑ Saito, Sakae; Aoki, Yuichi; Tamahara, Toru; Goto, Maki; Matsui, Hiroyuki; Kawashima, Junko; Danjoh, Inaho; Hozawa, Atsushi; Kuriyama, Shinichi; Suzuki, Yoichi; Fuse, Nobuo (2020). "Oral Microbiome Analysis in Prospective Genome Cohort Studies of the Tohoku Medical Megabank Project". Frontiers in Cellular and Infection Microbiology. 10: 604596. doi: 10.3389/fcimb.2020.604596 . ISSN   2235-2988. PMC   7878372 . PMID   33585276.
  14. ↑ Nagasaki, Masao; Yasuda, Jun; Katsuoka, Fumiki; Nariai, Naoki; Kojima, Kaname; Kawai, Yosuke; Yamaguchi-Kabata, Yumi; Yokozawa, Junji; Danjoh, Inaho; Saito, Sakae; Sato, Yukuto (21 August 2015). "Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals". Nature Communications. 6 8018. Bibcode:2015NatCo...6.8018.. doi:10.1038/ncomms9018. ISSN   2041-1723. PMC   4560751 . PMID   26292667.
  15. ↑ Kawai, Yosuke; Mimori, Takahiro; Kojima, Kaname; Nariai, Naoki; Danjoh, Inaho; Saito, Rumiko; Yasuda, Jun; Yamamoto, Masayuki; Nagasaki, Masao (October 2015). "Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals". Journal of Human Genetics. 60 (10): 581–587. doi:10.1038/jhg.2015.68. ISSN   1434-5161. PMC   4635170 . PMID   26108142.
  16. ↑ Tadaka, Shu; Saigusa, Daisuke; Motoike, Ikuko N.; Inoue, Jin; Aoki, Yuichi; Shirota, Matsuyuki; Koshiba, Seizo; Yamamoto, Masayuki; Kinoshita, Kengo (4 January 2018). "jMorp: Japanese Multi Omics Reference Panel". Nucleic Acids Research. 46 (D1): D551 –D557. doi:10.1093/nar/gkx978. ISSN   1362-4962. PMC   5753289 . PMID   29069501.
  17. ↑ Tadaka, Shu; Katsuoka, Fumiki; Ueki, Masao; Kojima, Kaname; Makino, Satoshi; Saito, Sakae; Otsuki, Akihito; Gocho, Chinatsu; Sakurai-Yageta, Mika; Danjoh, Inaho; Motoike, Ikuko N. (2019). "3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome". Human Genome Variation. 6 28. doi:10.1038/s41439-019-0059-5. ISSN   2054-345X. PMC   6581902 . PMID   31240104.
  18. ↑ Sakurai-Yageta, Mika; Kumada, Kazuki; Gocho, Chinatsu; Makino, Satoshi; Uruno, Akira; Tadaka, Shu; Motoike, Ikuko N.; Kimura, Masae; Ito, Shin; Otsuki, Akihito; Narita, Akira (12 October 2021). "Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs". Journal of Biochemistry. 170 (3): 399–410. doi:10.1093/jb/mvab060. ISSN   1756-2651. PMC   8510329 . PMID   34131746.
  19. ↑ "Genome information for 14,000 people is now available -jMorp 2021 major update-｜ToMMo". ToMMo ｜ Tohoku Medical Megabank Organization (in Japanese). 27 December 2021. Retrieved 1 July 2022.
  20. ↑ Otsuki, Akihito; Okamura, Yasunobu; Ishida, Noriko; Tadaka, Shu; Takayama, Jun; Kumada, Kazuki; Kawashima, Junko; Taguchi, Keiko; Minegishi, Naoko; Kuriyama, Shinichi; Tamiya, Gen; Kinoshita, Kengo; Katsuoka, Fumiki; Yamamoto, Masayuki (20 September 2022). "Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology". Communications Biology. 5 (1): 991. doi:10.1038/s42003-022-03953-1. ISSN   2399-3642. PMC   9489684 . PMID   36127505.
  21. ↑ "Completion of 50,000 Japanese whole genome sequence analysis and release of whole genome reference panel of 38,000 Japanese individuals (38KJPN)｜ToMMo". ToMMo ｜ Tohoku Medical Megabank Organization (in Japanese). 19 July 2022. Retrieved 13 October 2022.
  22. ↑ "jMorp". jmorp.megabank.tohoku.ac.jp. Retrieved 11 July 2023.
  23. ↑ Center (APRC), Asia and Pacific Research. "Whole genome analysis of 100,000 Japanese people to serve as foundation for personalized medicine and drug discovery". ScienceJapan. Retrieved 5 September 2024.
  24. ↑ "3.2. JG3.0.0 — jMorp User Guide documentation". jmorp.megabank.tohoku.ac.jp. Retrieved 25 August 2024.
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