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 |
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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 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Development of a single-cell analysis method for tumor-infiltrating lymphocytes with genomic abnormalities and elucidation of its clinical significance | JP21cm0106383 |
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 | PD-1 blockade therapy promotes infiltration of tumor-attacking exhausted T cell clonotypes | doi: 10.1016/j.celrep.2022.110331 | JGAD000391 |
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 |
