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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 ResearchDevelopment of Japonica Array NEO ~ Enabling application of genome analysis to a wider range of people ~ News Timeline all News Events Research Monthly archives 2024, April 2024, February 2024, January 2023, November 2023, October 2023, September 2023, August 2023, July 2023, June 2023, May 2023, April 2023, March 2023, January 2022, December 2022, November 2022, October 2022, September 2022, July 2022, May 2022, April 2022, January 2021, December 2021, November 2021, September 2021, August 2021, July 2021, June 2021, March 2021, January 2020, November 2020, October 2020, September 2020, August 2020, July 2020, June 2020, April 2020, March 2020, February 2020, January 2019, December 2019, November 2019, September 2019, August 2019, July 2019, May 2019, April 2019, March 2019, February 2019, January 2018, December 2018, November 2018, October 2018, September 2018, August 2018, July 2018, June 2018, May 2018, March 2018, February 2018, January 2017, December 2017, November 2017, October 2017, September 2017, August 2017, July 2017, June 2017, May 2017, March 2017, February 2017, January 2016, December 2016, November 2016, October 2016, September 2016, August 2016, July 2016, June 2016, May 2016, April 2016, March 2016, February 2016, January 2015, December 2015, November 2015, October 2015, September 2015, August 2015, July 2015, June 2015, May 2015, April 2015, March 2015, February 2015, January 2014, November 2014, October 2014, August 2014, July 2014, April 2014, March 2014, February 2014, January 2013, November 2013, August 2013, July 2013, June 2013, May 2013, April 2013, February 2013, January 2012, December 2012, November 2012, October 2012, September 2012, April 2012, March 2012, February Development of Japonica Array NEO ~ Enabling application of genome analysis to a wider range of people ~ Research: 2020/02/25 Summary ・ We have developed a novel disease-oriented SNP Array “Japonica ArrayTM NEO” equipped with variants unique to the Japanese population including disease-related SNPs and intended for the application in clinical use such as medical examinations. ・ SNP information obtained by Japonica ArrayTM NEO can be restored to more than 10 million of variant information using genotype imputation. ・ By the combination with genotype imputation, Japonica ArrayTM NEO makes it possible to obtain variant information comparable to whole genome sequencing at low cost, high speed, and high accuracy, which enables genome analysis for a much larger number of people. Outline Japonica ArrayTM, a tool for genomic analysis that enables us to obtain genome-wide information of Japanese individuals at low-cost and high accuracy, has been developed in the Tohoku University Tohoku Medical Megabank Organization (ToMMo). ToMMo designed a novel SNP array equipped with SNPs unique to the Japanese population including disease-related SNPs and the Thermo Fisher Scientific Japan Group has begun sale of the product as “Japonica ArrayTM NEO.” Japonica ArrayTM NEO includes more than 28,000 disease-related SNPs unique to Japanese individuals based on publications and detabases, and is expected to be widely used in association studies of disease risks. In addition, tagSNPs are designed based on the Japanese whole-genome reference panel, 3.5KJPNv2, and therefore, Japonica ArrayTM NEO is the best tool for genome analysis of Japanese population. Combined tagSNP information obtained by Japonica ArrayTM NEO with genotype imputation, it is possible to reconstruct variant information that is comparable to the one acquired by whole-genome sequence analysis. To obtain variant information at the level of whole-genome sequencing, which has been difficult to perform on large-scale populations due to its cost, now becomes a realistic option by virtue of Japonica ArrayTM NEO, and is expected to contribute to future research that aims to realize personalized medicine. Details ToMMo was the first in the world to perform a whole-genome analysis of a specific ethnic group on a scale of more than 1,000 individuals, and has published the results as a whole genome reference panel. This panel was utilized to design a microarray, and the Japonica ArrayTM (2014) and the Japonica ArrayTM v2 (2017) were developed by selecting SNPs that are optimized for the Japanese population to achieve high-performance genome analysis at a low cost. This time, we improved the method to design Japonica ArrayTM; tagSNP was selected based on the linkage disequilibrium statistics (r2), which is increasingly becoming the global standard. The design was based on 3.5KJPNv2, the largest whole-genome reference panel of Japanese individuals (3,552 people) ever developed. ・Number of SNPs on the array Approximately 650,000 tagSNPs of autosomes and X chromosomes, as optimized for genotype imputation for the Japanese population, were selected using linkage disequilibrium statistics (r2) based on the information of 3.5KJPNv2, and were then loaded into the array. On the other hand, the disease-related SNPs were selected based on published GWAS results by specialists and from other databases (GWAS Catalog) or commercially available with SNP arrays (UK Biobank Axiom Array), and then filtered by 3.5KJPNv2 to select approximately 28,000 SNPs present in Japanese population. In total, approximately 660,000 SNPs including tagSNPs and disease-related SNPs (some of them are overlapped in both groups) are installed on the array. ・Detailed information on performance The performance of Japonica ArrayTM NEO was verified by genotyping using samples derived from 286 Japanese individuals. As a results, 99.5% of the SNPs showed polymorphisms, demonstrating that the array was capable of efficiently detecting SNPs in Japanese. Moreover, by the genotype imputation using 3.5KJPNv2, the average value of the determination coefficient between the estimated SNP and that of input was 0.9 or more in nearly all minor allele frequency categories, demonstrating sufficient prediction accuracy. Moreover, the total number of imputed SNPs with a certain accuracy (INFO>0.8) or higher was approximately 13 million in total, which suggests that the design is useful for genome-wide genotyping of Japanese population.  ・Types of target diseases The array was designed to collect SNP information on Japanese in terms of a wide range of diseases, primarily common diseases, and to be capable of the association studies between SNPs and disease. The specific target diseases include neuropsychiatric disorders, such as dementia, depression, and autism spectrum disorders (approximately 5,500), cardiovascular diseases, such as hypertension, heart disease, and cerebrovascular disease (approximately 1,100), respiratory diseases, such as bronchial asthma and chronic obstructive pulmonary disease (approximately 2,000), metabolic diseases, such as diabetes and dyslipidemia (approximately 2,900), malignant neoplasms (approximately 900), and hereditary diseases (approximately 900). In addition to SNPs for specific diseases, HLA (human leukocyte antigen) and KIR (killer immunoglobulin receptor) (approximately 7,200 in total) involved in various immune regulation, pharmacogenomics (approximately 1,800), and other SNPs related to traits and gene expression, are also included. *Japonica Array NEO disease-related marker list is HERE Future outlook Despite the recent reducing costs for whole-genome sequence analysis, it is not easy to implement such analyses in fields beyond research. However, with the launch of Japonica ArrayTM NEO, the price hurdle has fallen for acquiring variant information on a genome-wide scale, and it may now be possible to identify the link between disease and a wider range of genomic information. Japonica ArrayTM NEO makes it possible to perform genome analysis at low cost for a large number of individuals, and it is expected to expand into new areas such as medical examinations, which have not yet been targeted for genome analysis. The differences in genomes among ethnic groups has been clarified, and we believe that Japonica ArrayTM NEO, which is more optimized for the Japanese population than conventional systems, will greatly contribute to the establishment of precision medicine and personalized healthcare in Japan.   Publication Details Title: Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs Authors: Mika Sakurai-Yageta, Kazuki Kumada, Chinatsu Gocho, Satoshi Makino, Akira Uruno, Shu Tadaka, Ikuko N Motoike, Masae Kimura, Shin Ito, Akihito Otsuki, Akira Narita, Hisaaki Kudo, Yuichi Aoki, Inaho Danjoh, Jun Yasuda, Hiroshi Kawame, Naoko Minegishi, Seizo Koshiba, Nobuo Fuse, Gen Tamiya, Masayuki Yamamoto, and Kengo Kinoshita Journal: Journal of Biochemistry Published date:13 May 2021 DOI: 10.1093/jb/mvab060     Related Link Methylome and transcriptome data, and disease-related markers list of Japonica Array NEO are now integrated into jMorp Japonica Array: Improved genotype imputation by designing a population-specific SNP array with 1,070 Japanese individuals News Timeline Tweet 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