Wikipedia

Tohoku Medical Megabank Project

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]

Tohoku Medical Megabank Project
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 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

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

Prospective cohort studies

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  • Community-based cohort.[1]

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]

  • Return of results to participants (including genomic information).[5]

Research projects

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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]

  • SNP array Genotyping.[6]

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

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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).[14]
  • Japonica array, a SNP array optimized for Japanese population by taking advantage of 1KJPN haplotype information, is released.[15]

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.[16]

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).[17]

2019

  • Japanese reference genome (JG1) is released (published in 2021).[10]
  • 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).[18]

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.[19]
  • JSV1, a structural variation panel, which is constructed with long-read sequencing data, is released.[20]

2022

  • Whole genome sequencing of 50,000 cohort participants was finished.[21]
  • Japanese genome reference panel (38KJPN) is released.

2023

  • Whole genome sequencing of 69,000 cohort participants was finished.[22]
  • Japanese genome reference panel (54KJPN) is released. Data is available through the portal site, jMorp.

2024

  • Whole genome sequencing of 100,000 cohort participants was finished.[23]
  • The Japanese reference genome (JG3.0.0), which has been significantly updated from JG2.0 based on Nanopore ultra-long s and PacBio HiFi data, has been released.[24]

References

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  1. ^ a b c d e f g 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. ^ a b c 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. ^ a b 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. ^ a b 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. doi:10.1038/s41588-024-01782-y.
  10. ^ a b 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. ^ a b 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. ^ a b 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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