Due to the replacement of the National Institute of Genetics Supercomputer System, all services related to the NBDC Human Database will be suspended during the following period: Expected from February 14th (Fri), 2025, to March 17 (Mon), 2025.
Please note that the suspension period may be extended by 2 weeks. We apologize for the inconvenience this may cause.
https://www.ddbj.nig.ac.jp/news/en/2025-02-06-e.html
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
hum0496.v1
NBDC Research ID: hum0496.v1
SUMMARY
Aims: Okinawa Bio-information Bank (OBi) is a bio resource bank that integrates human genomic DNA, plasma (or serum), and clinical information to elucidate the unique genetic background and disease susceptibility mechanisms of Okinawans.
Methods: We obtained imputed genotyping data for up to 9,235,975 SNPs. Association studies for the serum levels of ALT, AST, and GGT were performed in OBi and BioBank Japan (BBJ) separately , then these association data were combined by meta-analyses.
Participants/Materials: OBi Ryukyu population (n=8,715), BBJ Ryukyu population (n=7,004)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0496.v1.gwas.v1 | GWAS for serum levels of ALT, AST and GGT | Unrestricted-access | 2025/02/27 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
ALT: n=15,224 (OBi-Ryukyu n=8,440, BBJ-Ryukyu n=6,784) AST: n=15,203 (OBi-Ryukyu n=8,406, BBJ-Ryukyu n=6,797) GGT: n=14,496 (OBi-Ryukyu n=8,434, BBJ-Ryukyu n=6,062) |
| Targets | Genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform |
OBi: Illumina [Infinium Asian Screening Array v1.0 BeadChip] BBJ: Illumina [Infinium OmniExpress, HumanExome, Infinium OmniExpressExome v1.0, Infinium OmniExpressExome v1.2] |
| Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | - |
| Genotype Call Methods (software) |
minimac4 Imputation: reference 3,256 Japanese WGS from the BBJ and 2,504 individuals from the 1KGP (phase3v5) |
| Association Analysis & Meta Analysis (software) |
Association Analysis: BOLT-LMM (v.2.3.6) Meta Analysis: METAL software (v.2020-05-05) |
| Filtering Methods |
Sample QC: sample call rate ≧0.98 Genotyping QC: SNP call rate ≧ 0.98, MAF ≧ 0.01, p-values for Hardy–Weinberg equilibrium (HWE) test > 1×10−6 Imputation QC: MAF ≧ 0.005, Rsq ≧ 0.7 |
| Marker Number (after QC) |
ALT: 9,224,376 variants AST: 9,222,117 variants GGT: 9,235,975 variants |
| NBDC Dataset ID |
(Click the gwas number to download files) |
| Total Data Volume | 2.2 GB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shiro Maeda
Affiliation: Faculty of Medicine, University of the Ryukyus
Project / Group Name: -
| Name | Title | Project Number |
|---|---|---|
| Promotion project of innovation-eco system collaborating organization from the Okinawa prefecture | Disease Genome Research and Genomic Medicine for the Health and Longevity of Okinawans | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | A variant in HMMR/HMMR-AS1 is associated with serum alanine aminotransferase levels in the Ryukyu population | doi: 10.1038/s41598-025-90195-w | hum0496.v1.gwas.v1 |
hum0496.v1_release note
hum0496 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0496.v1 | 2025/02/27 | GWAS for serum levels of ALT, AST and GGT |
hum0496.v1
DNAs extracted from peripheral blood cells of OBi Ryukyu population (n=8,715) and BBJ Ryukyu population (n=7,004) were genotyped, imputed, and performed genome-wide association studies and meta-analyses (text file).
Note:
hum0267.v1_release note
hum0267 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0267.v1 | 2025/02/12 | NGS (RNA-seq) |
hum0267.v1
RNAs extracted from tumor tissues of 47 children who suspected of sarcoma were used for the RNA-sequencing analysis. Fastq files are provided.
Note：
hum0267.v1
NBDC Research ID: hum0267.v1
SUMMARY
Aims: Pediatric solid tumors are a diverse group of neoplasms, and accurate diagnosis of tumor subtype is necessary. The detection of disease-specific fusion genes such as EWSR1-FLI1 in Ewing Sarcoma and PAX3/7-FOXO1 in alveolar rhabdomyosarcoma, can improve the diagnosis of pediatric solid tumors. In addition, recent advances in techniques have identified several subtype-defining somatic genetic alterations, including internal tandem duplication of BCOR in clear cell sarcoma of the kidney, and MYOD1 p.Leu122Arg (p.L122R) in spindle cell/sclerosing rhabdomyosarcoma. In this study, we performed transcriptome analysis using RNA-sequencing to assess its clinical utility in the differential diagnosis of pediatric solid tumors.
Methods: We performed RNA-sequencing in 47 children who suspected of sarcoma and analyzed disease-specific gene alterations (include novel gene alterations).
Participants/Materials: Forty-seven children, who were suspicious of sarcoma.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000284 | NGS (RNA-seq) | Controlled-access (Type I) | 2025/02/12 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
47 children who suspected of sarcoma (ICD10) Rhabdomyosarcoma (C499): 19, Ewing sarcoma (C419): 8, Undifferentiated sarcoma (C499): 5, Malignant rhabdoid tumor (C809): 3, Myxopapillary ependymoma (C719): 2, Clear cell sarcoma of the kidney (C64), Fetal rhabdomyomatous Nephroblastoma (C64), Inflammatory myofibroblastic tumor (-), Langerhans cell histiocytosis (C966), Liposarcoma (C499), Malignant peripheral nerve sheath tumor (C479), Neuroblastoma (C749), NUT carcinoma (C80.9), Subcutaneous panniculitis-like T-cell lymphoma (C863), Synovial sarcoma (C499): 1 case each |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra RNA Library Prep Kit for Illumina |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp x 2 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000390 |
| Total Data Volume | 205.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Manabu Wakamatsu
Affiliation: Department of Pediatrics, Nagoya University Graduate School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrated diagnosis based on transcriptome analysis in suspected pediatric sarcomas | doi: 10.1038/s41525-021-00210-y | JGAD000390 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
hum0418.v1
NBDC Research ID: hum0418.v1
SUMMARY
Aims: Genome profiling to estimate both adverse events and response of chemotherapy in cancer patients
Methods: Genome profiling using next generation sequencers
Participants/Materials: Cancer patient who will receive chemotherapy
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000662 | NGS (Target Capture) | Controlled-access (Type I) | 2025/02/17 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
| Participants/Materials |
Cancer patient who will receive chemotherapy (ICD10: C00-D48): 507 cases 1018 samples tumor tissues and non-tumor tissues (peripheral blood cells): 1018 samples including 2 samples from 1 case having multiple cancers and 2 samples from 1 case having primary tumor and relapsed tumor |
| Targets | Target Capture |
| Target Loci for Capture Methods | NCC Oncopanel test (114 genes) |
| Platform | Illumina [MiSeq, NextSeq] |
| Library Source | DNA was extracted from tumor tissues and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) |
SureSelect XT reagent KAPA Hyper Prep kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000792 |
| Total Data Volume | 2.7 TB (fastq, bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takashi Kohno
Affiliation: Division of Genome Biology, National Cancer Center Research Institute
Project / Group Name: TOP-GEAR Project
URL: UMIN ID: UMIN000011141
https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000013046
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Program for an Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED) | Pan-Japan storage of clinical and genomic information on advanced solid and hereditary cancers for precision cancer medicine | JP18kk0205004 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Feasibility and utility of a panel testing for 114 cancer‐associated genes in a clinical setting: A hospital‐based study | doi: 10.1111/cas.13969 | JGAD000792 |
| 2 | A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing | doi: 10.1186/s13073-018-0547-0 | JGAD000792 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
