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
hum0394.v2
NBDC Research ID: hum0394.v2
SUMMARY
Aims: We perform spatial transcriptome analysis and other omics analyses, such as genome/epigenome sequencing and multiplexed immunofluorescence, using fresh-frozen and FFPE specimens of non-small cell lung cancers. We try to develop a novel stratification method for lung cancer patients by considering intratumor heterogeneity and conditions of complicated microenvironments of cancer tissues. We aim to characterize omics statuses of cancer cells and their surrounding stromal cells and immune cells, such as cancer-associated fibroblasts and tumor-infiltrating lymphocytes, at a spatial level and evaluate tumor cell-microenvironment relationships at a molecular level.
Methods: Spatial transcriptome sequencing Visium, high-performance in situ gene expression mapping Xenium, Multiplex Fluorescence Immunostaining, Whole Genome Sequencing and Targeted Long-Read Methylation Sequencing (t-nanoEM)
Participants/Materials:
[Visium] 16 tumor sections from 8 non-small cell lung cancer patients
[Xenium] Five tumor sections from 5 non-small cell lung cancer patients
[WGS] 1 tumor section and 1 non-tumor section from 1 non-small cell lung cancer patient
[t-nanoEM] Five microdissected tumor regions from 1 non-small cell lung cancer patient
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000613 |
NGS (Visium Spatial Gene Expression), Histological image |
Controlled-access (Type I) | 2024/04/08 |
| JGAS000757 | NGS (WGS, t-nanoEM) | Controlled-access (Type I) | 2024/11/20 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 8 cases surgical section: 16 samples |
| Targets | Visium Spatial Gene Expression |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from surgical sections (fresh-frozen/FFPE) |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression Reagent Kits |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
fresh-frozen: 118 bp FFPE: 78 bp |
| Software | spaceranger-1.2.1, spaceranger-1.3.0 |
| QC | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000742 |
| Total Data Volume | 479.7 GB (fastq, png, json, csv, tsv, mtx, cloupe, html) |
| Comments (Policies) | NBDC policy |
Xenium In Situ Gene Expression
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 5 cases surgical section: 5 samples |
| Targets | Xenium In Situ Gene Expression |
| Target Loci for Capture Methods | 302 genes (Human Lung panel: 202 genes, custom: 100 genes） |
| Platform | 10x Genomics [Xenium Analyzer] |
| Source | surgical sections (fresh-frozen/FFPE) |
| Cell Lines | - |
| Reagents (Panel, Kit, Version) |
Xenium Slides & Sample Prep Reagents Xenium Decoding Reagents Xenium Decoding Consumables |
| Software | xenium-1.1.0.2, xenium-1.2.0.3 |
| QC | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000742 |
| Total Data Volume | 479.7 GB (csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, zarr) |
| Comments (Policies) | NBDC policy |
Multiplex Fluorescence Immunostaining
| Participants/Materials |
lung adenocarcinoma (ICD10: C349): 3 cases tumor tissues: 3 samples |
| Targets | Multiplex Fluorescence Immunostaining |
| Target Loci for Capture Methods | cycle/probe information |
| Platform | Akoya Biosciences [PhenoCycler] |
| Library Source | tumor tissues of lung adenocarcinomas |
| Cell Lines | - |
| Cell Treatment Method (kit name) | Staining Kit for PhenoCycler |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000742 |
| Total Data Volume | 479.7 GB (qptiff) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 1 case tumor tissue: 1 sample (Illumina, Nanopore) non-tumor tissue: 1 sample (Illumina) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [NovaSeq 6000] Nanopore [PromethION] |
| Library Source | DNAs extracted from tumor tissue and non-tumor tissue |
| Cell Lines | - |
| Library Construction (kit name) |
Illumina: TruSeq Nano DNA Library Prep Kit, NEBNext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina Nanopore: Ligation Sequencing Kit V14 (SQK-LSK114) |
| Fragmentation Methods |
Illumina: Ultrasonic fragmentation (Covaris) Nanopore: - |
| Spot Type |
Illumina: Paired-end Nanopore: Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Illumina: 300 bp Nanopore: 7,500 bp on average |
| Mapping Methods |
Illumina: BWA-MEM Nanopore: Guppy |
| Mapping Quality | - |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | Illumina: x44 (non-tumor tissue), x82 (tumor tissue) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000898 |
| Total Data Volume | 616.6 GB (fastq, bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
non-small cell lung cancer (ICD10: C349): 1 case five microdissected tumor regions: 1 sample |
| Targets | t-nanoEM |
| Target Loci for Capture Methods | Twist Alliance Pan-cancer Methylation Panel - 1.5 MB |
| Platform | Nanopore [PromethION] |
| Source | DNA extracted from tumor tissue sample |
| Cell Lines | - |
| Library Construction (kit name) |
NEBNext Enzymatic Methyl-seq Kit The five libraries were pooled and subjected to target enrichment using the Twist Standard Hyb and Wash Kit v2 with a pan-cancer panel. |
| Fragmentation Methods | Covaris g-TUBE |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 4,800 bp on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000898 |
| Total Data Volume | 616.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Ayako Suzuki
Affiliation: Laboratory of Medical Omics Data Analysis, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Development of spatial genome and transcriptome analytical methods in local regions of lung cancer tissues | 21K15566 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
hum0394.v2_release note
hum0394 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0394.v2 | 2024/11/18 | NGS (WGS, t-nanoEM) |
| hum0394.v1 | 2024/04/08 | NGS (Visium Spatial Gene Expression), Xenium In Situ Gene Expression, Multiplex Fluorescence Immunostaining |
hum0394.v2
- 1 tumor section and 1 non-tumor section from 1 non-small cell lung cancer patient were used for Whole Genome Sequencing. Fastq and bam files are provided.
- 1 sample of five microdissected tumor regions from 1 non-small cell lung cancer patient were used for Targeted Long-Read Methylation Sequencing (t-nanoEM). Fastq files are provided.
hum0394.v1
- 16 tumor sections from 8 non-small cell lung cancer patients were used for Visium Spatial Gene Expression Assay. Fastq, png, json, csv, tsv, mtx, cloupe, and html files are provided.
- 5 tumor sections from 5 non-small cell lung cancer patients were used for Xenium In Situ Gene Expression Assay. Csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, and zarr files are provided.
- 3 tumor tissues from 3 non-small cell lung cancer patients were used for multiplex fluorescence immunostaining. Qptiff files are provided.
Note:
hum0466.v1_release note
hum0466 Release Note
| Research ID | Release Date | Type of Data |
|---|---|---|
| hum0466.v1 | 2024/11/20 | GWAS for the JPSC-AD study |
hum0466.v1
DNAs extracted from peripheral blood cells of 9,479 participants in the JPSC-AD study, were genotyped, imputed, and genome-wide association studies were performed (text file).
Note:
hum0466.v1
NBDC Research ID: hum0466.v1
SUMMARY
Aims: - Identification of risk and protective factors for dementia and depression
- Elucidation of the overall picture of risk and protective factors for dementia and depression
- Establishment of preventive strategy for dementia and depression
Methods: Genotyping, imputation, and genome-wide association study were performed.
Participants/Materials: Of the 9,479 community residents collected at the 8 facilities participating in the Japan Prospective Studies Collaboration for Aging and Dementia (JPSC-AD) study.
URL: https://www.eph.med.kyushu-u.ac.jp/jpsc/en/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0466.v1.gwas.v1 | GWAS for JPSC-AD study | Unrestricted-access | 2024/11/20 |
*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 | JPSC-AD study participants (ICD10: R90.8): 9,479 individuals |
| Targets | Genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Japanese Screening Array-24 v1.0 Consortium BeadChip [Illumina] |
| Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | - |
| Genotype Call Methods (software) |
Genotype call: GenomeStudio Genotype imputation: Minimac4 v1.0.0 Imputation reference panel: whole genome sequences of 1,037 (BioBank Japan) and 2,504 (1000 Genomes Project (Phase 3v5)) (hum0014) |
| Association Analysis & Meta Analysis (software) | BOLT-LMM |
| Filtering Methods |
Sample QC: Gender discrepancy, sample call rate <98%, close relatives, and outliers (distance > 10sd short, 11sd long) were excluded. Genotyping QC: Hardy-Weinberg equilibrium >1.0x10-6, call rate >99%, monomorphic, minor allele count <5, and frequency difference >6% with reference panel were excluded. Post-imputation QC: Variants with minor allele frequency (MAF) <0.5% and Rsq <0.7 were excluded. |
| Marker Number (after QC) | 8,495,153 variants |
| NBDC Dataset ID |
(Click the gwas number to download files) |
| Total Data Volume | 153.6 MB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshiharu Ninomiya
Affiliation: Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University
Project / Group Name: JPSC-AD study
URL: https://www.eph.med.kyushu-u.ac.jp/jpsc/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Research and Development Grants for Dementia, Japan Agency for Medical Research and Development (AMED) | Genome and Neuroimaging Research on Dementia Based on Large-Scale Prospective Cohort Data | JP24dk0207053 |
| Suntory Holdings Limited | - | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Common protein-altering variant in GFAP is associated with white matter lesions in the older Japanese population. npj Genomic Med | doi: 10.1038/s41525-024-00431-x | hum0466.v1.gwas.v1 |
hum0272.v3
NBDC Research ID: hum0272.v3
SUMMARY
Aims: Analysis of gene expression and somatic gene mutation in tumor cells and immune cells using skin tumor samples such as melanoma
Methods: whole exome sequencing analysis, RNA sequencing analysis, scRNA sequencing analyses, scTCR sequencing analyses, and target capture sequencing
Participants/Materials: melanoma patients: 4 + 9 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000285 | Controlled-access (Type I) | 2021/12/20 | |
| JGAS000285 (Data addition) | Controlled-access (Type I) | 2022/02/07 | |
| JGAS000589 | NGS (Target Capture) | Controlled-access (Type I) | 2024/11/13 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
melanoma (ICD10: C439): 4 cases cultured tumor cells established from melanoma patients: 4 cases, 4 + 1 samples lymph node metastatic lesions: 1 case, 2 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from cultured tumor cells and lymph nodes |
| Cell Lines | - |
| Library Construction (kit name) | Hybrid Selection |
| Fragmentation Methods | Captured / Adaptor ligation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 92 bp (mean) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000391 |
| Total Data Volume | 99.6 + 628.8 GB (bam [ref: hg38]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
melanoma (ICD10: C439): 4 cases cultured tumor cells established from melanoma patients: 4 cases, 4 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from cultured tumor cells |
| Cell Lines | - |
| Library Construction (kit name) | Hybrid Selection |
| Fragmentation Methods | Captured / Adaptor ligation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp (mean) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000391 |
| Total Data Volume | 99.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
melanoma (ICD10: C439): 3 cases tumor-infiltrating lymphocyte (TIL): 2 cases, 3 samples peripheral blood lymphocyte (PBL): 2 cases, 2 samples lymph node tumor-infiltrating lymphocyte (LN-TIL): 1 case, 2 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from TIL, PBL and LN-TIL |
| Cell Lines | - |
| Library Construction (kit name) | Single Cell Immune Profiling Solution Kit |
| Fragmentation Methods | Hybrid Selection |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp (mean) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000391 |
| Total Data Volume | 628.8 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
melanoma (ICD10: C439): 12 cases tumor cells: 19 samples peripheral blood cells: 12 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | Precision ID mtDNA Whole Genome Panel |
| Platform | Thermo Fisher Scientific [Ion Torrent Proton] |
| Library Source | DNAs extracted from tumor cells and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 107 bp (mean) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000717 |
| Total Data Volume | 11.3 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takashi Inozume
Affiliation: Department of Dermatology, Chiba University
Project / Group Name: Development of more effective immunotherapy for skin cancer
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Identification of essential biomarkers for efficacy of anti-PD-1 therapy | 19K08744 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Analysis of tumor-specific T cells aimed at overcoming challenges with immune checkpoint inhibitors | 22K08424 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Analysis of PD-1+ tumor-infiltrating T cells according to cancer antigen hierarchy | 20H03694 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | TIGIT/CD155 axis mediates resistance to immunotherapy in patients with melanoma with the inflamed tumor microenvironment | doi: 10.1136/jitc-2021-003134 | JGAD000391 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000391 | 2022/12/26-2025/03/31 |
| Takuya Yamamoto | Laboratory of Precision Immunology, National Institutes of Biomedical Innovation, Health and Nutrition | Japan | Basic research for vaccine development against gastrointestinal cancer and malignant melanoma based on the identification of novel cancer antigens | JGAD000391 | 2024/11/12-2025/09/01 |
