Japan’s National Center Biobank Network Tops 250,000 Participants and 800,000 Biospecimens

Behind the walls of Japan’s most advanced specialized hospitals, a quiet industrial-scale operation has been running for more than a decade: the collection, freezing, cataloguing, and distribution of human biospecimens from hundreds of thousands of patients. A new review published in Frontiers in Genetics by Yosuke Omae and Katsushi Tokunaga of the National Center Biobank Network (NCBN) now offers the most detailed accounting yet of what this infrastructure has achieved through Japanese fiscal year 2025, and the numbers are striking. As of the end of March 2026, the network has registered more than 250,000 participants and amassed over 800,000 human biospecimens, spanning more than 200 disease types, making it Japan’s leading disease-oriented biobank in both quality and quantity.

The NCBN is not a single facility but a federated network of six biobanks operated by Japan’s National Centers for advanced and specialized medicine, supported by the Ministry of Health, Labour and Welfare. Four of these centers sit in the Tokyo metropolitan area, with the remaining two in the Osaka and Aichi regions. Each center pairs a specialized hospital with a research institute and a disease-based biobank focused on conditions with major national health impact: cancer at the National Cancer Center (NCC), cardiovascular and cerebrovascular disease at the National Cerebral and Cardiovascular Center (NCVC), psychiatric and neurological disorders at the National Center of Neurology and Psychiatry (NCNP), pediatric and obstetric conditions at the National Center for Child Health and Development (NCCHD), and age-related diseases at the National Center for Geriatrics and Gerontology (NCGG). In April 2025, the network underwent a structural transformation when the National Center for Global Health and Medicine merged with the National Institute of Infectious Diseases to form the Japan Institute for Health Security (JIHS), bringing the Central Biobank Secretariat and the infectious disease biobank under this new umbrella while NCBN activities continued uninterrupted.

What distinguishes these resources from ordinary sample collections is the depth and traceability of the clinical information attached to them. The primary sample types are blood and DNA, but depending on disease characteristics the biobanks also collect cerebrospinal fluid, frozen tissue, and other specialized biospecimens. Every sample is accompanied by clinical records curated by the physicians of each center, and quality-related preanalytical information, including collection, processing, aliquoting, and storage times as well as nucleic acid quality indicators, can be provided to users on request. Some samples now carry whole-genome sequencing data, positioning the network as a unique platform for translational research, biomarker discovery, and genomic medicine in Japan. A centralized NCBN Catalogue Database allows researchers to search for available bioresources across all six biobanks in one place, with recent enhancements adding exclusion searches and support for ICD-10 subclassification queries.

Utilization of the stored samples has accelerated in parallel with registration. Cumulatively, more than 200,000 human biospecimens accompanied by clinical information have been provided to companies and academic institutions, with the NCGG biobank alone having distributed over 81,000 biospecimens through collaborative research and more than 31,000 through fee-based provision. The network offers two usage models: collaborative research with NCBN institutions, and provision, which requires a fee covering actual costs but grants the user ownership of resulting intellectual property. The NCC began offering provision in 2025, expanding an option previously available at four centers. Samples are currently available to overseas users through joint research with any NCBN biobank, and efforts are underway, in consultation with other Japanese biobanks, to establish direct provision systems for foreign institutions.

The review highlights representative discoveries that illustrate the distinctive strengths of each biobank. At the NCC, the largest cancer biobank in Japan, whole-genome sequencing of clear cell renal cell carcinoma samples as part of the International Cancer Genome Consortium produced a remarkable finding: a mutational signature of unknown cause appears in more than 70 percent of cases in Japan but in less than 2 percent elsewhere, indicating the existence of multiple, geographically variable mutagenic exposures that shaped cancer genomes differently across populations. The biobank has also collected large numbers of rare cancers, including brain, ophthalmic, head and neck cancers, and bone and soft tissue sarcomas, which are difficult to assemble at other institutions.

At the NCVC, researchers began collecting time-series samples from the same subjects at multiple time points, spanning the hyperacute to chronic phases of ischemic heart disease, in 2019. Analysis of genomic and clinical data, including echocardiographic measurements, revealed that a specific mutation in the RNF213 gene, already associated with moyamoya disease among Asians, may also be linked to changes in cardiac-to-pulmonary blood flow and an increased risk of refractory pulmonary hypertension. This finding has contributed to the development of genetic testing that may improve disease prevention and treatment. Meanwhile, the NCNP Biobank maintains one of the largest and most extensively characterized disease-oriented cerebrospinal fluid collections in Japan. Building on induced pluripotent stem cell work suggesting that elevated BMP4 protein concentration causes neurogenesis failure in Alzheimer’s disease, researchers used biobank CSF from patients and healthy individuals to confirm elevated BMP4 concentrations in patients, providing mechanistic insight into cognitive decline.

The JIHS Biobank, the only general hospital resource within the network, contributed samples to the international COVID-19 Host Genetics Initiative. An exome-wide association study drawing on 21 cohorts across 12 countries, including rare variant analyses of 5,085 severe COVID-19 cases and 571,737 controls, identified a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 that increases the risk of severe COVID-19 by 5.3-fold. At the NCCHD, whole-genome DNA methylation data from patients with gonadotropin deficiency and unaffected controls revealed a patient-specific methylation change in the promoter region of the ZNF254 gene, which may help explain the pathogenesis of this neuroendocrine disorder. The NCCHD biobank is also uniquely suited as a source of control samples, since it collects detailed pregnancy and delivery histories from normal deliveries alongside rare pediatric disease cases, often spanning genomic DNA from two or three generations of affected families.

At the NCGG, researchers conducted a genome-wide association study using genomic data from patients with dementia with grain, Alzheimer’s disease, and cognitively healthy older adults, identifying a genomic locus associated with dementia with grain at genome-wide significance. Integrating gene expression data from the human brain through expression quantitative trait loci analysis revealed a strong association with DAPK2 gene expression in the frontal lobe, marking the first study to identify risk genes for this condition and deepening understanding of dementias with complex clinical presentations. The NCGG has also developed an integrated database for dementia research capable of combining clinical records, imaging data, and omics data for large-scale analysis.

Beyond disease samples, the NCBN has completed whole-genome sequencing of 9,850 control samples with support from the Japan Agency for Medical Research and Development, creating a dataset called NCBN Control. Sequenced samples were selected based on ICD-10 codes to establish control data for Japan’s national genomics initiative on cancer and rare disease. The dataset captured notable genetic diversity, including the Ryukyuan population, whose genetic background differs from that of mainland Japanese. Statistical polymorphism information is publicly available in the NBDC Human Database and MGeND, and individual genome data have been shared under 28 collaborative studies, with nine published papers already using the data as non-cancer controls, for variant filtering, and as imputation reference panels.

Quality assurance has become a global benchmark for the field. The International Organization for Standardization published the first edition of the biobank standard ISO 20387 in 2018, and in Japan the Japan Accreditation Board began accrediting biobanks in 2023 based on the corresponding JIS Q 20387 standard. In March 2024, four Japanese biobanks, including the NCGG and NCNP biobanks within the NCBN, received accreditation for the first time, and expansion to the remaining NCBN biobanks is under consideration. Together with Biobank Japan and the Tohoku Medical Megabank, the NCBN contributes to a comprehensive national research infrastructure through the All-Japan framework called Biobank Network Japan. While those other initiatives provide large-scale population and genomic resources, the NCBN offers unique access to deeply phenotyped patients, rare diseases, specialized bioresources, and longitudinal clinical information, positioning it as a vital platform for advancing precision medicine in Japan.

Subject of Research: Genetics

Article Title: Recent achievements of the National Center Biobank Network (NCBN) bioresources through Japanese fiscal year 2025

Article References: Omae, Y., & Tokunaga, K. (2026). Recent achievements of the National Center Biobank Network (NCBN) bioresources through Japanese fiscal year 2025. Frontiers in Genetics, 17, Article 1910504. https://doi.org/10.3389/fgene.2026.1910504

Image Credits: AI Generated

DOI: 10.3389/fgene.2026.1910504

Keywords: biobank, genomics, precision medicine, Japan, whole-genome sequencing, Recent, achievements, National, Center, Network, NCBN, bioresources