[Suspension of NBDC Human Database activity during the New Year Holidays] DBCLS will be closed for the New Year Holidays from December 27, 2025 (Sat) to January 5, 2026 (Mon).
After January 6 (JST), we will respond to requests or questions which are received during this period.
We sincerely apologize for any inconvenience this may cause and thank you for your kind understanding and cooperation.
We are currently receiving a large number of Applications for data submission, and the review process is taking longer than usual.
We sincerely apologize for the delay and kindly ask for your understanding.
When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.
About NBDC Human Database
An enormous amount of human data is being generated with advances in next-generation sequencing and other analytical technologies. We therefore need rules and mechanisms for organizing and storing such data and for effectively utilizing them to make progress in the life sciences.
To promote sharing and utilization of human data while considering the protection of personal information, the Database Center for Life Science (DBCLS) of the Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS-DS) created a platform for sharing various data generated from human specimens, which are available for publicly access in cooperation with the DNA Data Bank of Japan
.
You can apply to use or submit human data through this website.
Violators of the guidelines who have not submitted a report on the deletion of Controlled-access data shall be disclosed here.
What's New
hum00552.v1
NBDC Research ID: hum0552.v1
SUMMARY
Aims: Abdominal aortic aneurysm(AAA) is a localized dilation of the abdominal aorta that may rupture and cause sudden death. In Japan, "aortic aneurysm and dissection" ranks around the 10th leading cause of mortality. Recent studies have shown that clonal hematopoiesis (CH), an age-related expansion of hematopoietic stem cells carrying somatic mutations in genes such as DNMT3A, TET2, ASXL1, PPM1D, JAK2, SF3B1, SRSF2, and TP53, can promote atherosclerosis and thrombosis, contributing to cardiovascular disease. While such mutations are common in patients with atherosclerotic disease and heart failure, their role in AAA remains unclear. This study aims to establish an AAA patient database and clarify how CH affects disease severity and treatment response.
Methods: target capture sequencing
Participants/Materials: Forty-four patients underwent their first surgical repair for abdominal aortic aneurysm at Nagoya University Hospital. AAA (including both fusiform and saccular types) is defined as an abdominal aortic diameter of ≥3 cm on CT imaging.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000864 | NGS (Target Capture) | Controlled-access (Type I) | 2025/12/23 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
abdominal aortic aneurysm (ICD10: I71.3, I71.4): 44 cases peripheral blood: 44 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods |
ASXL1 (11–13), ATM (1–63), CBL (8–9), CHEK2 (2–15), DNMT3A (1–23), EZH2 (2–20), GNB1 (5–7), JAK2 (12–16), PHF6 (2–10), PPM1D (6), RUNX1 (1–9), SF3B1 (13–18), SMC1A (1–25), SRSF2 (2), TET2 (3–11), TP53 (1–11) numbers reveal exon numbers |
| Platform | Illumina [NovaSeq X] |
| Library Source | DNAs extracted from peripheral blood |
| Cell Lines | - |
| Library Construction (kit name) | VariantPlex, MBC adapter kit for Illumina |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001007 |
| Total Data Volume | 100.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yoshimitsu Yura
Affiliation: Department of Cardiology, Nagoya University School of Medicine
Project / Group Name: Clonal Hematopoiesis & Cardiovascular Disease Project
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Mechanistic elucidation of how clonal hematopoiesis modifies cardiovascular disease | 24K19026 |
| Fusion Oriented REsearch for disruptive Science and Technology (FOREST) program, Japan Science and Technology Agency (JST) | Elucidation of the pathophysiology of age-associated cardiovascular disease mediated by clonal hematopoiesis | JPMJFR2217 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Tet2-Clonal Hematopoiesis Drives Aortic Aneurysm via Macrophage-to-Osteoclast-like Differentiation | JGAD001007 | |
| 2 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
hum0552.v1_release note
hum0552 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0552.v1 | 2025/12/23 | NGS (Target Capture) |
hum0552.v1
DNAs extracted from peripheral blood cells of 44 patients with abdominal aortic aneurysm were used for the target capture sequencing analysis. Fastq files are provided.
Note:
hum0430.v1_release note
hum0430 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0430.v1 | 2025/12/02 | NGS (RNA-seq, Exome) |
hum0430.v1
DNA/RNA extracted from the colorectal cancer, colorectal adenoma, and normal intestinal mucosa samples obtained from patients with colorectal cancer, colorectal adenoma patients, and healthy individuals were used for the whole exome sequencing and RNA sequencing analyses. Fastq files are provided.
Note:
hum00430.v1
NBDC Research ID: hum0430.v1
SUMMARY
Aims: Colorectal cancer is the most common type of cancer in Japan. Although some colorectal cancers have a genetic background, most colorectal cancers are sporadic. Known risk factors for colorectal cancer include smoking, obesity, lack of exercise, and intake red or processed meat. Furthermore, although it has been suggested that changes in the intestinal environment due to changes in diet and lifestyle may be involved in the increased incidence of colorectal cancer in Japan, the molecular mechanism has not yet been fully elucidated. The main objective of this study is to elucidate the changes in the intestinal environment that cause colorectal tumors.
Methods: Research biopsies were obtained from the tumor, normal mucosa 1-2 cm away from the tumor, terminal ileum, cecum, ascending colon, descending colon, and sigmoid colon to rectum using a lower gastrointestinal endoscopy for participants. DNA/RNA was extracted from the samples and used for RNA-seq and whole exome sequencing analyses.
Participants/Materials:
RNA-seq: 14 patients with advanced colorectal cancer, 41 patients with early stage colorectal cancer, 6 patients with colorectal adenoma, and 17 healthy individuals
Exome: 24 patients with advanced colorectal cancer (including 14 same cases in RNA-seq), 23 patients with early stage colorectal cancer (including 20 same cases in RNA-seq)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000655 | NGS (RNA-seq, Exome) | Controlled-access (Type I) | 2025/12/02 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
advanced colorectal cancer (ICD10: C189): 14 cases colorectal cancer: 14 samples, colorectal adenoma: 1 sample, normal intestinal mucosa: 65 samples early stage colorectal cancer (ICD10: C189): 41 cases colorectal cancer: 38 samples, colorectal adenoma: 5 samples, normal intestinal mucosa: 160 samples colorectal adenoma (ICD10: D126): 6 cases colorectal adenoma: 11 samples, normal intestinal mucosa: 33 samples 17 healthy individuals normal intestinal mucosa: 61 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNA extracted from colorectal cancer, colorectal adenoma, and normal intestinal mucosa samples |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000785 |
| Total Data Volume | 1.1 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
advanced colorectal cancer (ICD10: C189): 24 cases colorectal cancer: 25 samples, colorectal adenoma: 1 sample, normal intestinal mucosa: 24 samples early stage colorectal cancer (ICD10: C189): 23 cases colorectal cancer: 23 samples, colorectal adenoma: 6 samples, normal intestinal mucosa: 23 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from colorectal cancer, colorectal adenoma, and normal intestinal mucosa samples |
| Cell Lines | - |
| Library Construction (kit name) | Illumina DNA Prep with Enrichment, Twist Comprehensive Exome Panel |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000785 |
| Total Data Volume | 1.0 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shinichi Yachida
Affiliation: Division of Cancer Genomics, National Cancer Center Research Institute
Project / Group Name: Establishment of an Endoscopic Biopsy Repository for Comprehensive Characterization of the Gut Microenvironment in Colorectal Diseases and Its Application to Exploratory Translational Research
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| National Cancer Center Research and Development Fund | Establishment of a comprehensive metagenomic database of the gut microbiota in colorectal cancer patients and individuals at high risk for cancer development: A multi-institutional collaborative study | 2020-A-4 |
| National Cancer Center Research and Development Fund | Establishment of the infrastructure for a multicenter biobank of fecal and comprehensive gastrointestinal endoscopic biopsy specimens | 2023-A-6 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Development of target-selective mid-size drugs using cyclic peptide derivatives | 20H03362 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Studies on the elucidation of intestinal environmental changes in colorectal tumorigenesis via the serrated pathway | 23H02892 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Research aimed at elucidating alterations in the intestinal microenvironment associated with colorectal cancer development in high-risk individuals, and the development of personalized preventive strategies based on these findings | JP22ck0106546 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Development of personalized colorectal cancer prevention strategies through integrated profiling of the gut microbiome using stool and endoscopic biopsy specimens in ultra-high-risk populations | JP23ck0106799 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Research and development aimed at predicting the occurrence of adverse effects associated with anticancer drugs through comprehensive analysis of the gut microbiota | JP21cm0106477 |
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Development of biomarkers for early detection and susceptibility assessment of young-onset colorectal cancer through comprehensive analysis of the intestinal microenvironment | JP23ama221404 |
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Elucidation of the pathogenetic mechanisms underlying early-onset colorectal cancer through integrated analyses of diet, gut microbiota, and mucosal inflammation, and the development of novel susceptibility and early diagnostic strategies | JP24ama221430 |
| Research Program on the challenges of Global Health issues, Japan Agency for Medical Research and Development (AMED) | Investigation of infection-associated cancers conducted within the framework of the Japan–U.S. Medical Cooperation Program | JP23jk0210009 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Development of novel strategies for prevention, diagnosis, and treatment through comprehensive genomic analysis of rare cancers, including sarcomas and brain tumors | JP24ck0106877 |
| Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University | - | - |
| Joint Research Project of the Institute Medical Science, the University of Tokyo | Investigation of the role of the gut microbiota in the serrated pathway, a novel colorectal carcinogenesis mechanism | - |
| Takeda Science Foundation | Elucidation of colorectal carcinogenesis mechanisms and development of preventive strategies based on gut microbiome dynamics toward the implementation of microbiome-driven precision medicine | - |
| Yasuda Medical Foundation | Elucidation of the mechanisms underlying colorectal carcinogenesis based on gut microbiome dynamics | - |
| The Mitsubishi Foundation | Identification of gut microbial agents involved in colorectal tumorigenesis and elucidation of their underlying mechanistic pathways | - |
| Princess Takamatsu Cancer Research Fund | Investigation of the impact of gut microorganisms on the pathogenesis of colorectal cancer | - |
| Yakult Bio-Science Foundation | Investigation of intestinal microenvironment modulation for the prevention of colorectal cancer | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Variability in non-tumor areas of colorectal cancer patients as revealed by endoscopic intestinal step biopsies | doi: 10.1186/s12943-024-02159-9 | JGAD000785 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
hum0405.v3
NBDC Research ID: hum0405.v3
SUMMARY
Aims: In recent years, "cancer stem cells" have been reported to exist in many cancers. Many reports have shown that they are the main cause of cancer recurrence. The aim of this study is to test whether cancer stem cells can be identified using patient samples. We will perform omics analysis of rare pediatric cancers by integrating genomics, transcriptomics, proteomics and metabolomics, including somatic and germline mutations, to deepen our understanding of the biological characteristics of the target disease. Based on the knowledge gained and clinical information from patients, we will conduct preclinical pharmacological studies using mouse models and in vitro models to investigate the therapeutic effects of novel therapeutic agents and novel therapeutic strategies such as cellular therapies.
Methods: WES, RNA-seq and Small RNA-seq
Participants/Materials:
Pediatric B-cell precursor acute lymphocytic leukemia: 69 cases
Pediatric acute myeloid leukemia: 9 cases
B-cell precursor acute lymphocytic leukemia patients who received tisagenlecleucel: 16 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000623 | Controlled-access (Type I) | 2023/12/25 | |
| JGAS000631 | Controlled-access (Type I) | 2025/07/16 | |
| JGAS000760 | NGS (RNA-seq) | Controlled-access (Type I) | 2025/12/02 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
Pediatric B-cell precursor acute lymphocytic leukemia (ICD10: C910): 64 cases leukemia cells from peripheral blood or bone marrow fluid: 64 samples Pediatric acute myeloid leukemia (ICD10: C920): 3 cases whole blood or bone marrow aspirates at the time of remission or relapse: 6 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400RS] |
| Library Source | DNAs extracted from leukemia cells |
| Cell Lines | - |
| Library Construction (kit name) | Lotus DNA Library Prep Kit, xGen Exome Research Panel |
| Fragmentation Methods | Restriction enzyme reaction |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Genomon v2.6.2 |
| Mapping Quality | Reads and variants with MAPQ< 20 or base call quality< 15 were excluded. |
| Reference Genome Sequence | GRCh37 |
| Coverage (Depth) | 129 |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000752: Pediatric B-cell precursor acute lymphocytic leukemia JGAD000761: Pediatric acute myeloid leukemia |
| Total Data Volume |
JGAD000752: 935.2 GB (fastq) JGAD000761: 180.6 GB (bam, bai) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pediatric B-cell precursor acute lymphocytic leukemia (ICD10: C910): 69 cases leukemia cells from peripheral blood or bone marrow fluid: 69 samples Pediatric acute myeloid leukemia (ICD10: C920): 9 cases (5 cases revealed pediatric B-cell precursor acute lymphocytic leukemia at onset and Pediatric acute myeloid leukemia at relapse） whole blood or bone marrow aspirates at disease onset or relapse: 15 samples B-cell precursor acute myeloid leukemia (ICD10: C91.3): 16 cases T cells in each patient's infusion product sorted into CD38-CD73-Tim-3-HLA-DR+ (4 marker-defined; 4MD) fraction: 13 samples non-4MD fractions: 16 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [HiSeq X] MGI [DNBSEQ-G400RS] |
| Library Source | RNAs extracted from leukemia cells or T-cells |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II Directional RNA Library Prep Kit for Illumina |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Genomon v2.6.2/v2.6.3 |
| Mapping Quality | unmapped reads < 5% |
| Reference Genome Sequence | GRCh37 |
| Coverage (Depth) | Uniquely mapped reads >90% |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000752: Pediatric B-cell precursor acute lymphocytic leukemia JGAD000761: Pediatric acute myeloid leukemia JGAD000901: B-cell precursor acute myeloid leukemia |
| Total Data Volume |
JGAD000752: 935.2 GB (fastq) JGAD000761: 180.6 GB (bam, bai) JGAD000901: 271.6 GB (bam, bai) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pediatric B-cell precursor acute lymphocytic leukemia (ICD10: C910): 69 cases leukemia cells from peripheral blood or bone marrow fluid: 69 samples |
| Targets | small RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 550] |
| Library Source | RNAs extracted from leukemia cells |
| Cell Lines | - |
| Library Construction (kit name) | NEXTflex Small RNA Sequencing kit v3 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD00752 |
| Total Data Volume | 935.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Junko Takita
Affiliation: Department of Pediatrics, Graduate School of Medicine, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Study of spatiotemporal variety of intractable pediatric cancers and development of new drugs | JP22ama221505 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Development of novel therapeutic strategies for intractable pediatric cancers based on the multi-omics information | 17H04224 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Integrated analysis of mechanisms of genetic susceptibility to cancer and clonal evolution in pediatric cancer | 20H00528 |
| KAKENHI Grant-in-Aid for Challenging Research (Exploratory) | Development of novel therapeutic strategies for pediatric solid tumor based on non-driver gene targeted approaches | 21K19405 |
| KAKENHI Grant-in-Aid for Challenging Research (Exploratory) | Elucidation of crosstalk between neurodevelopmental disorders and tumorigenesis and development of novel therapeutic drugs | 23K18264 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Clarification of spatio-temporal diversity for overcoming cancers that develop from childhood to young adulthood | 24H00628 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | RNA-seq-based miRNA signature as an independent predictor of relapse in pediatric B-cell acute lymphoblastic leukemia | doi: 10.1182/bloodadvances.2023011583 | JGAD000752 |
| 2 | Multi-omics analysis identifies an M-MDSC-like immunosuppressive phenotype in lineage-switched AML with KMT2A rearrangement | doi: 10.1038/s41467-025-63271-y | JGAD000761 |
| 3 | CAR-T cells with the CD38-CD73-Tim-3-HLA-DR+ phenotype predict the efficacy of tisagenlecleucel as a treatment for B cell precursor ALL | JGAD000901 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
