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
“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.
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, 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.
You can access the former versions of our genome reference panel, such as 1KJPN, 2KJPN, 3.5KJPN on Integrative Japanese Genome Variation Database (iJGVD), and after 3.5KJPNv2 on Japanese Multi Omics Reference Panel (jMorp).
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.
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.
You can access the former versions of the Japanese reference genome v1 (JRGv1) released on 2016, or v2 (JRGv2) released on 2017 with a long-read-type next-generation sequencer, PacBio RSII (Pacific Biosciences).
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 around 50 thousand 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 53,000 adults. We also measured 4,599 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.
Since 2020, methylome and transcriptome 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. Transcriptome data, such as those for lymphoblastoid cell lines (LCLs) using long-read sequencing technology (PacBio Isoform-Sequencing; Iso Seq), and also CD4+ T cell, monocyte and neutrophil; is readily accessible on jMorp, or through our Genome Browser.
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 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.
-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)
-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)
-3/11, Disaster Medicine, & ToMMo: Perspectives from the Executive Director (Interview with Dr. Yamamoto, November 10, 2015)
We use the next-generation genome sequencer to analyze the whole genome sequences of the part of cohort participants.
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