Medicine: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) Makoto Sasaki (Executive Director, IMM)
Established2012

The Tohoku Medical Megabank Project is a national project in Japan.[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] It started in 2012.

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

  • Community-based cohort (General population).[1]
  • Birth and Three-generation cohort.[1]
  • Biobanking and database.[2][4]
  • Return of results to participants (including genomic information).[5]

Research projects

  • Whole genome sequencing with short read and long read technologies.[6]
  • SNP array Genotyping with Japonica array.[6]
  • Construction of Japanese human genome reference.[7]
  • Plasma metabolome analysis with NMR and Mass spectrometry.[8]
  • Proteome analysis.[8]
  • Transcriptome analysis.[9]
  • Epigenome analysis.[9]
  • Oral Microbiome analysis.[10]

Timeline

2013

  • Recruitment of TMM Community-Based Cohort starts.[1]
  • Recruitment of TMM Birth and Three-Generation Cohort Study starts.[1]

2014

  • Japanese genome reference panel (1KJPN), which shows variant allele frequency based on whole genome sequencing of 1,070 cohort participants, is released (draft version 2014, official version 2015).[11]
  • Japonica array, a SNP array optimized for Japanese population by taking advantage of 1KJPN haplotype information, is released.[12]

2015

  • A portal site of Japanese Multi Omics Reference Panel (jMorp), providing metabolome and proteome data from the cohort participants, is opened. As of 2022, jMorp covers metabolome, proteome, transcriptome, methylome, as well as genome reference panel.[13]

2016

  • Recruitment of TMM Community-Based Cohort is finished with over 80,000 participants.[1]

2017

  • Recruitment of TMM Birth and Three-Generation Cohort Study is finished with over 70,000 participants.[1]
  • The second followup survey starts.

2018

  • Japanese genome reference panel (3.5KJPNv2), which shows variant allele frequency based on whole genome sequencing of 3,554 cohort participants, is released (published in 2019).[14]

2019

  • Japanese reference genome (JG1) is released (published in 2021).[7]
  • Distribution of 67,000 TMM Community-Based Cohort samples data starts.
  • Japanese genome reference panel (4.7KJPN) is released.
  • Japonica array NEO, a SNP array optimized for Japanese population by taking advantage of 3.5KJPN haplotype information, is released (published in 2021).[15]

2020

  • Distribution of 54,000 SNP array data starts.
  • Distribution of TMM Birth and Three-Generation Cohort samples data starts.
  • Japanese genome reference panel (8.3KJPN) is released.
  • Japanese reference genome (JG2) is released.

2021

  • The third followup survey starts.
  • Japanese genome reference panel (14KJPN) is released.[16]
  • JSV1, a structural variation panel, which is constructed with long-read sequencing data, is released.[17]

2022

  • Whole genome sequencing of 50,000 cohort participants was finished.[18]
  • Japanese genome reference panel (38KJPN) is released.

2023

  • Whole genome sequencing of 69,000 cohort participants was finished.[19]
  • Japanese genome reference panel (54KJPN) is released. Data is available through the portal site, jMorp.

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Kuriyama, Shinichi; Yaegashi, Nobuo; Nagami, Fuji; Arai, Tomohiko; Kawaguchi, Yoshio; Osumi, Noriko; Sakaida, Masaki; Suzuki, Yoichi et al. (2016). "The Tohoku Medical Megabank Project: Design and Mission". Journal of Epidemiology 26 (9): 493–511. doi:10.2188/jea.JE20150268. PMID 27374138. PMC 5008970. https://www.jstage.jst.go.jp/article/jea/26/9/26_JE20150268/_article. 
  2. ↑ 2.0 2.1 Minegishi, Naoko; Nishijima, Ichiko; Nobukuni, Takahiro; Kudo, Hisaaki; Ishida, Noriko; Terakawa, Takahiro; Kumada, Kazuki; Yamashita, Riu et al. (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. https://www.jstage.jst.go.jp/article/tjem/248/1/248_45/_article. 
  3. ↑ Kuriyama, Shinichi; Metoki, Hirohito; Kikuya, Masahiro; Obara, Taku; Ishikuro, Mami; Yamanaka, Chizuru; Nagai, Masato; Matsubara, Hiroko et al. (2020-02-01). "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. PMID 31504573. PMC 7124511. https://doi.org/10.1093/ije/dyz169. 
  4. ↑ Ogishima, Soichi; Nagaie, Satoshi; Mizuno, Satoshi; Ishiwata, Ryosuke; Iida, Keita; Shimokawa, Kazuro; Takai-Igarashi, Takako; Nakamura, Naoki et al. (2021-12-10). "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. PMID 34887386. 
  5. ↑ Kawame, Hiroshi; Fukushima, Akimune; Fuse, Nobuo; Nagami, Fuji; Suzuki, Yoichi; Sakurai-Yageta, Mika; Yasuda, Jun; Yamaguchi-Kabata, Yumi et al. (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. https://pubmed.ncbi.nlm.nih.gov/34234266. 
  6. ↑ 6.0 6.1 Yasuda, Jun; Kinoshita, Kengo; Katsuoka, Fumiki; Danjoh, Inaho; Sakurai-Yageta, Mika; Motoike, Ikuko N.; Kuroki, Yoko; Saito, Sakae et al. (2019-02-01). "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. https://pubmed.ncbi.nlm.nih.gov/30452759. 
  7. ↑ 7.0 7.1 Takayama, Jun; Tadaka, Shu; Yano, Kenji; Katsuoka, Fumiki; Gocho, Chinatsu; Funayama, Takamitsu; Makino, Satoshi; Okamura, Yasunobu et al. (2021-01-11). "Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference". Nature Communications 12 (1): 226. doi:10.1038/s41467-020-20146-8. ISSN 2041-1723. PMID 33431880. Bibcode: 2021NatCo..12..226T. 
  8. ↑ 8.0 8.1 Koshiba, Seizo; Motoike, Ikuko; Saigusa, Daisuke; Inoue, Jin; Shirota, Matsuyuki; Katoh, Yasutake; Katsuoka, Fumiki; Danjoh, Inaho et al. (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. 
  9. ↑ 9.0 9.1 Furukawa, Ryohei; Hachiya, Tsuyoshi; Ohmomo, Hideki; Shiwa, Yuh; Ono, Kanako; Suzuki, Sadafumi; Satoh, Mamoru; Hitomi, Jiro et al. (2016-05-19). "Intraindividual dynamics of transcriptome and genome-wide stability of DNA methylation". Scientific Reports 6: 26424. doi:10.1038/srep26424. ISSN 2045-2322. PMID 27192970. Bibcode: 2016NatSR...626424F. 
  10. ↑ Saito, Sakae; Aoki, Yuichi; Tamahara, Toru; Goto, Maki; Matsui, Hiroyuki; Kawashima, Junko; Danjoh, Inaho; Hozawa, Atsushi et al. (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. PMID 33585276. 
  11. ↑ Nagasaki, Masao; Yasuda, Jun; Katsuoka, Fumiki; Nariai, Naoki; Kojima, Kaname; Kawai, Yosuke; Yamaguchi-Kabata, Yumi; Yokozawa, Junji et al. (2015-08-21). "Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals". Nature Communications 6: 8018. doi:10.1038/ncomms9018. ISSN 2041-1723. PMID 26292667. Bibcode: 2015NatCo...6.8018.. 
  12. ↑ Kawai, Yosuke; Mimori, Takahiro; Kojima, Kaname; Nariai, Naoki; Danjoh, Inaho; Saito, Rumiko; Yasuda, Jun; Yamamoto, Masayuki et al. (October 2015). "Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals" (in en). Journal of Human Genetics 60 (10): 581–587. doi:10.1038/jhg.2015.68. ISSN 1434-5161. PMID 26108142. 
  13. ↑ Tadaka, Shu; Saigusa, Daisuke; Motoike, Ikuko N.; Inoue, Jin; Aoki, Yuichi; Shirota, Matsuyuki; Koshiba, Seizo; Yamamoto, Masayuki et al. (2018-01-04). "jMorp: Japanese Multi Omics Reference Panel". Nucleic Acids Research 46 (D1): D551–D557. doi:10.1093/nar/gkx978. ISSN 1362-4962. PMID 29069501. 
  14. ↑ Tadaka, Shu; Katsuoka, Fumiki; Ueki, Masao; Kojima, Kaname; Makino, Satoshi; Saito, Sakae; Otsuki, Akihito; Gocho, Chinatsu et al. (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. PMID 31240104. 
  15. ↑ Sakurai-Yageta, Mika; Kumada, Kazuki; Gocho, Chinatsu; Makino, Satoshi; Uruno, Akira; Tadaka, Shu; Motoike, Ikuko N.; Kimura, Masae et al. (2021-10-12). "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. PMID 34131746. 
  16. ↑ "Genome information for 14,000 people is now available -jMorp 2021 major update-｜ToMMo" (in ja). 2021-12-27. https://www.megabank.tohoku.ac.jp/english/genome-information-for-14000-people-is-now-available-jmorp-2021-major-update/. 
  17. ↑ Otsuki, Akihito; Okamura, Yasunobu; Ishida, Noriko; Tadaka, Shu; Takayama, Jun; Kumada, Kazuki; Kawashima, Junko; Taguchi, Keiko et al. (2022-09-20). "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. PMID 36127505. 
  18. ↑ "Completion of 50,000 Japanese whole genome sequence analysis and release of whole genome reference panel of 38,000 Japanese individuals (38KJPN)｜ToMMo" (in ja). 2022-07-19. https://www.megabank.tohoku.ac.jp/english/completion-of-50000-japanese-whole-genome-sequence-analysis-and-release-of-whole-genome-reference-panel-of-38000-japanese-individuals-38kjpn/. 
  19. ↑ "jMorp". https://jmorp.megabank.tohoku.ac.jp/help/history. 

External links




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