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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
hum00404.v1
NBDC Research ID: hum0404.v1
SUMMARY
Aims: In this study, we analyze the genomic information of samples from patients with various cardiovascular diseases, including severe heart failure, and identify genetic mutations and polymorphisms that are thought to be related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions. The source of the genome to be analyzed is mainly peripheral blood, but in some cases, the genome extracted from the myocardial tissue obtained by myocardial biopsy or iPS cells generated from the patient is also used. In the analysis using iPS cells, we repair genetic mutation using genome editing technology such as CRISPR/Cas9 and analyze the pathological phenotypes.
Methods:
[scRNA-seq] GFP (Control) or S-RBD-sfGFP was added to iPS cell-derived cardiomyocytes and after 48 hours the cells were collected and single-cell RNA sequence analysis was performed.
[WGS] Genomic DNA was extracted from the peripheral blood cells of cardiomyopathy cases and performed whole genome sequencing analysis.
Participants/Materials: iPS cell-derived cardiomyocytes established from a cardiomyopathy case, peripheral blood cells of 3 cardiomyopathy cases
URL: http://www.cardiology.med.osaka-u.ac.jp/?page_id=34330
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000620 | NGS (scRNA-seq) | Controlled-access (Type I) | 2025/09/30 |
| E-GEAD-628 | NGS (scRNA-seq) | Unrestricted-access | 2025/09/30 |
|
JGAS000704 JGAS000705 JGAS000706 |
NGS (WGS) | Controlled-access (Type I) | 2025/09/30 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
cardiomyopathy (ICD10: I42.0): 1 case GFP or S-RBD-sfGFP was added to iPS cell-derived cardiomyocytes generated from a cardiomyopathy case: 2 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Library Source | RNAs extracted from iPS cell-derived cardiomyocytes |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 3' Reagent Kits v3.1 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Mapping Methods | Cell Ranger v7.0.1 |
| Reference Genome Sequence | refdata-cellranger-GRCh38-3.0.0 |
| Detecting method for read count (software) | Cell Ranger v7.0.1 |
| QC Methods |
Unique Molecular Identifiers (UMI): 10–17 (Log2) UMIs per Barcode. Thresholds for genes expressed: more than seven (Log2) genes per barcode. Thresholds for mitochondrial UMI: Remove the barcodes with more than 20% of mitochondrial UMI counts. |
| Gene Number |
GFP: 23,234 S-RBD-sfGFP: 23,349 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000749 |
| Genomic Expression Archive ID | E-GEAD-628 |
| Total Data Volume |
JGAD000749: 66.7 GB (fastq) E-GEAD-628: 133 MB (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
cardiomyopathy (ICD10: I42.0): 3 cases hypertrophic cardiomyopathy (HCM): 1 case arrhythmogenic right ventricular cardiomyopathy (ARVC): 1 case myotonic dystrophy: 1 case |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from peripheral blood |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-Free Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
HCM: JGAD000837 ARVC: JGAD000838 myotonic dystrophy: JGAD000839 |
| Total Data Volume |
JGAD000837: 62.8 GB (fastq) JGAD000838: 64.3 GB (fastq) JGAD000839: 67.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shuichiro Higo
Affiliation: Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | SARS-CoV-2 spike receptor-binding domain is internalized and promotes protein ISGylation in human induced pluripotent stem cell-derived cardiomyocytes | doi: 10.1038/s41598-023-48084-7 | E-GEAD-628 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
hum0404.v1_release note
hum0404 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0404.v1 | 2025/09/30 | NGS (scRNA-seq, WGS) |
hum0404.v1
- RNAs extracted from the cells collected after 48 hours from adding GFP or S-RBD-sfGFP to iPS cell-derived cardiomyocytes generated from a cardiomyopathy case were used for single-cell RNA-sequencing analysis. Fastq, barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files are provided.
- DNAs extracted from peripheral blood of 3 cardiomyopathy cases were used for whole genome sequencing analysis. Fastq files are provided.
Note：
hum0533.v1_release note
hum0533 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0533.v1 | 2025/10/17 | NGS (Exome, RNA-seq) |
hum0533.v1
DNA/RNA extracted from tumor tissues or non-tumor tissues from 7 GAPPS patients were used for the whole exome sequencing and RNA sequencing analyses. Bam, bai and csv files are provided.
Note:
hum00533.v1
NBDC Research ID: hum0533.v1
SUMMARY
Aims: In recent years, gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS), an autosomal dominant syndrome with polyp formation in the gastric cardia progressing to carcinoma, has been reported. Germline mutations in APC promoter 1B were identified as its cause, yet the molecular mechanisms of carcinogenesis remain unclear. To elucidate the progression from normal mucosa to fundic gland polyps (FGPs) and carcinoma, we collected multiple samples from each lesion and performed whole exome sequencing and RNA sequencing. Comprehensive mutational and transcriptomic analyses provided novel insights into GAPPS biology.
Methods: Whole exome sequencing, RNA sequencing
Participants/Materials: 7 GAPPS cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000843 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2025/10/17 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
GAPPS (ICD10: D139): 7 cases 61 samples (14 gastric carcinoma, 13 gastric polyp, 27 normal gastric mucosa, 7 peripheral blood) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from tumor tissues or non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Software | GATK (v4.2.6.1), Picard MarkDuplicates (v2.27.5), Samtools (v1.14), ANNOVAR (2020-06-08 release) |
| Mapping Quality | Median MAPQ ≥ 60 |
| Reference Genome Sequence | GRCh38.p14 |
| Coverage (Depth) | 175x (range 144–236x) |
| QC Methods |
FastQC (v0.11.9) SNP: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0 INDEL: QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000985 |
| Total Data Volume | 653.9 GB（bam, bai, csv） |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
GAPPS (ICD10: D139): 7 cases 53 samples (13 gastric carcinoma, 13 gastric polyp, 27 normal gastric mucosa) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNA extracted from tumor tissues or non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II RNA Library Prep Kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Softwear | STAR (v2.7.10a), RSEM (v1.3.3), Samtools (v1.14), DESeq2 (v1.38.3) |
| Mapping Quality | Median MAPQ ≥ 60 |
| Reference Genome Sequence | GRCh38.p14 |
| QC Methods |
FastQC (v0.11.9) SNP: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0 INDEL: QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000985 |
| Total Data Volume | 653.9 GB（bam, bai, csv） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Chihiro Matsumoto
Affiliation: Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Princess Takamatsu Cancer Research Fund | Molecular elucidation of the dysplasia–adenoma–adenocarcinoma sequence in gastric cancer | 21-25303 |
| Japanese Gastric Cancer Association | Comprehensive genomic analysis for molecular mechanism of carcinogenesis of hereditary gastric cancer | JGCA-32 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Elucidation of the carcinogenic mechanisms of hereditary gastric cancer and establishment of innovative therapeutic strategies | 24K10427 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Development of a precise method for estimating the timing of mutations during carcinogenesis | 24K18481 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genomic and transcriptomic landscape of carcinogenesis in patients with gastric adenocarcinoma and proximal polyposis of the stomach (GAPPS) | ||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
hum0225.v2
NBDC Research ID: hum0225.v2
SUMMARY
Aims: Estimating the risks of developing adult T-cell leukemia (ATL) through a genetic analysis of human T-cell leukemia virus (HTLV-1)-associated myelopathy (HAM)
Methods: Target capture sequencing, RNA-seq, ATAC-seq, single-cell Multiome (scRNA-seq, scATAC-seq)
Participants/Materials:
Target capture: HAM 21 cases (infected and uninfected cells)
RNA-seq: HAM 13 cases (infected cells)
ATAC-seq: HAM 2 cases (infected cells)
scMultiome: HAM 2 cases, asymptomatic HTLV-1 carriers 3 individuals
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000226 | NGS (Target Capture) | Controlled-access (Type I) | 2020/05/08 |
| JGAS000835 | NGS (RNA-seq, ATAC-seq, scMultiome) | Controlled-access (Type I) | 2025/09/24 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
HAM（ICD-10：A858/B973）： 21 cases (46 samples) infected cells (tumor cells): 23 samples (including post-ATL specimens for 2 cases) uninfected cells (non-tumor cells): 23 samples (including post-ATL specimens for 2 cases) |
| Targets | Target Capture |
| Target Loci for Capture Methods | 280 genes (human) including 50 candidate genes for ATL and whole genome of HTLV-1 provirus |
| Platform | Illumina [HiSeq 2500/3000] |
| Library Source | DNAs extracted from PBMC (infected and uninfected cells) of HAM patients |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT HS Target Enrichment System |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000318 |
| Total Data Volume | 238 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | HAM（ICD-10：A858/B973）： 13 cases |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from HTLV-1-infected T cells sorted using anti-CD4, anti-CADM1, and anti-CD7 antibodies |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext rRNA Depletion Kit |
| Fragmentation Methods | chemical fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000977 |
| Total Data Volume | 583.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | HAM（ICD-10：A858/B973）： 2 cases |
| Targets | ATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from HTLV-1–infected T cells sorted using anti-CD4, anti-CADM1, and anti-CD7 antibodies |
| Cell Lines | - |
| Library Construction (kit name) | Standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000977 |
| Total Data Volume | 583.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
HAM（ICD-10：A858/B973）： 2 cases HTLV-1-infected asymptomatic individuals: 3 cases |
| Targets | scRNA-seq, scATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs/RNAs extracted from peripheral blood mononuclear cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell Multiome ATAC + Gene Expression |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
scRNA-seq: 118 bp scATAC-seq: 99 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000977 |
| Total Data Volume | 583.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Makoto Yamagishi / Yoshihisa Yamano
Affiliation: Graduate School of Frontier Sciences, The University of Tokyo / Institute of Medical Science, St. Marianna University School of Medicine
Project / Group Name: Laboratory of Viral Oncology and Genomics / Department of Rare Disases Research
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED) | Development of risk stratification and prevention for HTLV-1-associated diseases based on multi-omics database | JP20fk0108126 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Analysis of genome/epigenome control mechanism that regulates abnormal traits of HTLV-1 infected cells in HAM | 19H03575 |
| Practical Research Project for Rare / Intractable Diseases, Japan Agency for Medical Research and Development (AMED) | The establishment of evidence for clinical guideline development on HAM and HTLV-1-related refractory disease through integration of patient registry | JP19ek0109356 |
| Research Program on Emerging and Re-emerging Infectious Diseases, Japan Agency for Medical Research and Development (AMED) | Comprehensive study on elucidation of pathogenesis of HTLV-1 infection based on genome information and development of risk prediction algorithm | JP25fk0108672 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Mortality and risk of progression to adult T-cell leukemia/lymphoma in patients with HTLV-1-associated myelopathy/tropical spastic paraparesis | doi: 10.1073/pnas.1920346117 | JGAD000318 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Masao Matsuoka | Kumamoto University School of Medicine Hematology, Rheumatology and Infectious Diseases | Japan | Retrospective observational study of characteristics, clinical course and treatment of malignant lymphoma and adult T-cell leukemia/lymphoma with genetic and pathological evaluations | JGAD000318 | 2022/05/16-2030/03/31 |
