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About Mission and Outline Background Activities For Community Message from Executive Director Toward the Development of Personalized Healthcare through the Promotion of Industry-Academia Collaboration Organization and Members Department of Community Medical Supports Department of Preventive Medicine and Epidemiology Department of Biobank Department of Integrative Genomics Department of Health Record Informatics Department of Education and Training Department of Public Relations and Planning General Affairs and Planning Sector Cohort Studies Sector Integrated Biobank Sector Integrated Omics Sector Group of Planning Group of Public Relations Group of Education and Training Group of Return of Genomic Results Center for Promotion of Cohort Studies Center for Health Survey Promotion Group of Brain Imaging and Research Group of Biobank Center for Biobank Utilization and Academia-Industry Partnership Group of Integrated Database Systems Group of Information Management for Genome-Cohort Study Group of Privacy Controls Group of Sequencing Group of Microarray-based Genotyping Group of Metabolomics Group of Metagenomics and Microbiome Group of Omics Data Analysis Center for Genome-Wide Association Study Office of Nihonbashi Branch Operation Center for Genome Platform Projects Policy Site Policy Social Media Policy Research Cohort Study and Biobank Community-Based Cohort Study (TMM CommCohort Study) Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study) Integrative Genomics Publications Facilities and Equipment Researchers Specimen and Data Collection Ethical Issues ToMMo's Library News Timeline sitemap links access & contact JAPANESE Large Small A A Top ResearchIntegrative Genomics Integrative Genomics Research Activities With the aim of advancing personalized medicine and personalized prevention, we conduct genome analyses of biological specimens provided by cohort studies using next-generation sequencer. We also conduct omics analyses of protein and low-molecular metabolites using NMR machines, mass spectrometer, amongst other instruments. This data is processed using a super computer and other technologies.  In parallel with these analyses, we are developing technologies to analyze biological specimens, as well as software and information analysis methodologies for processing large quantities of data, including genome data. We have completed whole genome sequence analysis for 69,000 Japanese in 2023. This is one of the largest whole genome sequence analyses of a general population in the world.  We have furthermore developed a tool for analyzing the genomes of Japanese people, which has allowed the analysis of quasi-whole-genome sequences of Japanese people (Japonica Array). Key Word: Whole genome sequence, Population genetics, Genome reference panel, Japanese reference sequence, Metabolomics, Bioinformatics, High performance computing Publications The structural origin of metabolic quantitative diversitySeizo Koshiba, Ikuko Motoike, Kaname Kojima, Takanori Hasegawa,Matsuyuki Shirota, Tomo Saito, Daisuke Saigusa, Inaho Danjoh, Fumiki Katsuoka, Soichi Ogishima, Yosuke Kawai, Yumi Yamaguchi-Kabata, Miyuki Sakurai, Sachiko Hirano, Junichi Nakata, Hozumi Motohashi, Atsushi Hozawa, Shinichi Kuriyama, Naoko Minegishi, Masao Nagasaki, Takako Takai-Igarashi, Nobuo Fuse, Hideyasu Kiyomoto, Junichi Sugawara, Yoichi Suzuki, Shigeo Kure, Nobuo Yaegashi, Osamu Tanabe, Kengo Kinoshita, Jun Yasuda & Masayuki YamamotoScientific Reports 6, Article number: 31463 (2016); doi:10.1038/srep31463article 3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosomeShu Tadaka, Fumiki Katsuoka, Masao Ueki, Kaname Kojima, Satoshi Makino, Sakae Saito, Akihito Otsuki, Chinatsu Gocho, Mika Sakurai-Yageta, Inaho Danjoh, Ikuko N. Motoike, Yumi Yamaguchi-Kabata, Matsuyuki Shirota, Seizo Koshiba, Masao Nagasaki, Naoko Minegishi, Atsushi Hozawa, Shinichi Kuriyama, Atsushi Shimizu, Jun Yasuda, Nobuo Fuse, the Tohoku Medical Megabank Project Study Group, Gen Tamiya, Masayuki Yamamoto & Kengo KinoshitaHuman Genome Variation volume 6, Article number: 28 (2019); doi:10.1038/s41439-019-0059-5article Estimating carrier frequencies of newborn screening disorders using a whole-genome reference panel of 3552 Japanese individualsYumi Yamaguchi-Kabata, Jun Yasuda, Akira Uruno, Kazuro Shimokawa, Seizo Koshiba, Yoichi Suzuki, Nobuo Fuse, Hiroshi Kawame, Shu Tadaka, Masao Nagasaki, Kaname Kojima, Fumiki Katsuoka, Kazuki Kumada, Osamu Tanabe, Gen Tamiya, Nobuo Yaegashi, the Tohoku Medical Megabank Project Study Group, Kengo Kinoshita, Masayuki Yamamoto, Shigeo KureHuman Genetics, April 2019, Volume 138, Issue 4, pp 389–409; doi:10.1007/s00439-019-01998-7article Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project.Seizo Koshiba, Ikuko Motoike, Daisuke Saigusa, Jin Inoue, Matsuyuki Shirota, Yasutake Katoh, Fumiki Katsuoka, Inaho Danjoh, Atsushi Hozawa, Shinichi Kuriyama, Naoko Minegishi, Masao Nagasaki, Takako Takai‐Igarashi, Soichi Ogishima, Nobuo Fuse, Shigeo Kure, Gen Tamiya, Osamu Tanabe, Jun Yasuda, Kengo Kinoshita, Masayuki YamamotoGenes to Cells, April 2018, 2018; 23 (6): 406-417; doi:10.1111/gtc.12588article Other Major Publications (genome and omics analyses)   Database Japanese Multi Omics Reference Panel (jMorp) “jMorp” is a database consisted of genome, metabolome and proteome data in plasma. Multiple omics analysis data obtained by ToMMo is integrated to “jMorp”, and opened to the researchers online. Details of jMorp datasets jMorp User Guide Genome Variation Based on our study, the Japanese Whole Genome Reference Panel, referred to as 54KJPN, consisting of allele and genotype frequency panels from approximately 54,000 Japanese individuals that are estimated to be unrelated to each other out of 69,000 individuals who have completed whole genome analyses, has been published in the database jMorp. SNVs of interest can be searched for on our platform by the reference SNP ID number (rsID), Gene Symbol and locate information on the international human genome reference sequence. All found SNVs frequencies in our reference panel are displayed and can be compared with gnomAD. All the frequencies and locate information are downloadable by a single file for each chromosome. In addition to enhancements of jMorp, it includes such as X chromosome data, mitochondria data, Copy Number Variations (CNV) data, and implementation of the variant-structure mapping visualization tool. In addition, "JSV1", which covers large-scale base insertions and deletions called structural variants, has also been released on jMorp. structural variants of 111 trio have been analyzed and applied in research on SNVs. To date, there is few research on structural variants in the world. The release of JSV1 is anticipated to facilitate the understanding of genomic structural variants. Achievement of Research Product by Whole Genome Reference Panel: Japonica Array The “Japonica Array”, DNA microarray designed for genome analysis of Japanese population, was developed in 2014 by ToMMo, and has been used for our genome analyses of tens of thousands of cohort participants. ToMMo further designed a novel SNP array equipped with more than 28,000 SNPs unique to the Japanese population, including disease-related SNPs, known as the ‘Japonica Array NEO’. Additionally, tagSNPs are designed based on the Japanese whole-genome reference panel, 3.5KJPNv2, and hence, a whole genome sequence can be imputed very precisely with the Japonica Array NEO. Sakurai-Yageta M, Kumada K, Gocho C, et al. Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs. The Journal of Biochemistry. 2021; 170 (3): 399-410. Genome Sequence ToMMo has released the Japanese reference genome, JG1, constructed by integrating three de novo assembled genomes of Japanese male individuals in 2019. In 2020, we released updated version JG2, constructed by integrating six de novo assembled genomes from three Japanese male individuals. In January 2022, the JGS2.1.0 succeeded JG2.0.0. beta, where the successor utilizes GRCh38-derived sequences that have been patched for undetermined regions. The Japanese reference genome is available online. Metabolome and Proteome On “jMorp”, the results of global metabolome analysis for metabolites in plasma and proteome analysis are available online. You can find the distribution and frequencies information for major metabolites for more than 60,000 populations and proteins for several hundred populations. Metabolome data were measured by proton NMR and LC-MS in plasma obtained from participants from the population based cohort by the Tohoku Medical Megabank Project. Proteome data were obtained by nanoLC-MS. Metabolome and proteome data were obtained from more than 60,000 adults. We also measured around 4,500 volunteers for NMR metabolome analysis of samples at a repeat assessment survey. We have measured several thousand metabolites, including the uncharacterized ones and several hundred proteins by now. The data will be released after carefully checking each metabolite and protein in order. Transcriptome Transcriptome analysis of approximately 500 Japanese whole blood samples is on jMorp. Also, lymphoblastoid cell lines (LCLs) using long-read sequencing technology (PacBio Isoform-Sequencing; Iso Seq) is readily accessible on jMorp, or through our Genome Browser. Methylome Since 2020, methylome data from the iMethyl database has been integrated into jMorp. The Iwate Tohoku Medical Megabank Organization (IMM) analyzed methylation / gene expression using three types of cells (monocytes, CD4+ T cells, and neutrophils) across over 100 participants.  Phenome (PGx, Metagenome) Incorporating both pharmacogenomics (PGx) and the metagenome, relative abundances of microbial taxonomy identified by 16S rRNA V3-V4 region amplicon sequencing in saliva and dental plaques obtained from 1,388 volunteers, and microbiome analysis data of fecal samples obtained from 315 volunteers can also be found on jMorp. In terms of PGx, analyses of changes in enzyme activity for 382 enzymes with genetic polymorphisms involving amino acid substitutions related to drug sensitivity, can also be found.   ToMMo adopt a method called “data-visiting” which means researchers can reach and directly access the data themselves. You can check how we promoting data utilization. More detail is HERE   Press Releases -Researchers Investigate the Dietary Impacts of Dairy within the Japanese Population (Apr. 18, 2024) -Constructing the First Version of the Japanese Reference Genome(Jan. 29, 2021) -2020 major update of Japanese Multi Omics Reference Panel "jMorp": JG2 Japanese Reference Genome, 8.3KJPN allele frequency panel, and 25K Metabolome(Oct. 5, 2020) -2019 major update of Japanese Multi Omics Reference Panel "jMorp":15,000 people metabolome data and 4.7K Japanese individual genome variation(Sep. 13, 2019) -The Japanese reference genome, JG1, constructed by integrating three de novo assembled genomes of Japanese male individuals (Feb. 25, 2019) -Genetic Diversity of Enzymes Alters Metabolic Individuality (Sep. 2, 2016) -Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals (Aug. 21, 2015) -Japonica Array: Improved genotype imputation by designing a population-specific SNP array with 1,070 Japanese individuals (June 25, 2015) -Partial release of data from Tohoku Medical Megabank Project's Whole Genome Reference Panel (Aug. 29, 2014) -Tohoku Medical Megabank Organization high-accuracy whole genome sequencing of 1,000 healthy Japanese people: A base to search for the causes of diseases-Collection of over 15 million new gene polymorphisms- (Nov. 29, 2013) News -Metabolome, transcriptome, metagenome, and genome data expansion -jMorp 2023 major update- (Sep. 4, 2023) -The analysis of the whole genome sequence of 69,000 individuals has been completed, and 54KJPN is now available (Jul. 28, 2023) -Construction of Structural Variation Panel for Japanese Population Using Long-read Sequencing Technology (Oct. 11, 2022) -jMorp Update and User Interface Changes (September 2022) (Oct. 3, 2022) -Completion of 50,000 Japanese whole genome sequence analysis and release of whole genome reference panel of 38,000 Japanese individuals (38KJPN) (July 19, 2022) -Genome information for 14,000 people is now available -jMorp 2021 major update- (Dec. 27, 2021) -Allele frequency data of the 8.3KJPN has been released from dbSNP (June 29, 2021) -New article about design and development of a novel version of the SNP Array for the Japanese population, Japonica Array NEO was published (June 25, 2021) -The article about transcriptome analysis using a long-read sequencing technology (Nov. 12, 2020) -Development of Japonica Array NEO ~ Enabling application of genome analysis to a wider range of people ~ (Feb. 25, 2020) -Methylome and transcriptome data, and disease-related markers list of Japonica Array NEO are now integrated into jMorp (Jan. 16, 2020) -The linkage disequilibrium map (ToMMo_LD_map_192v1) has been released (Dec. 6, 2019) -Change of the data access control of 3.5KJPNv2, allele frequency data in Japanese genome reference panel, to open category (Jan. 25, 2019) -Expanded version of Japanese genome reference panel including INDEL allele is available online (Jan. 15, 2019) -New version of Japanese Multi Omics Reference Panel "jMorp": 10,719 people Metabolome data are now available online (Sep. 6, 2018) -Expanded version of Japanese genome reference panel including mitochondria and X chromosome is available online (June 25, 2018) -New expanded version of Japanese Multi Omics Reference Panel "jMorp": 5,093 people Metabolome data are now available online (Oct. 3, 2017) -The locations and allele frequencies of SNVs of 3,554 Japanese individuals by whole genome sequences is available (Sep. 28, 2017) -Announcing release of JRG v2 and decoyJRGv2 (June 6, 2017) -We enlarged Japanese Multi Omics Reference Panel "jMorp", 1,008 people Metabolome data are now online (Sep. 12, 2016) -Announcing release of JRG v1 (Aug. 25, 2016) -Release of locations and allele frequencies of all SNVs in whole genome sequences of 2,049 Japanese individuals (June 21, 2016) -Access for the locations and allele frequencies of all SNVs in the Whole Genome Reference Panel (Dec. 10, 2015)     Movies We use the next-generation genome sequencer to analyze the whole genome sequences of the part of cohort participants. and more movies HERE About Mission and Outline Background Activities For Community Message from Executive Director Organization and Members Policy Research Cohort Study and Biobank Integrative Genomics Publications Facilities and Equipment Researchers Ethical Issues Specimen &＃038; Data Collection ToMMo's Library News Timeline access & contact sitemap links JAPANESE Large Small A A Copyright(C) Tohoku University Tohoku Medical Megabank Organization All Rights Reserved. sitemap access & contact About Research Ethical Issues Specimen &＃038; Data Collection ToMMo's Library News Timeline access & contact sitemap links Japanese