NBDC Research ID: hum0470.v1
SUMMARY
Aims: The aim of this study is to investigate the prognosis of patients with urothelial carcinoma who have undergone immunotherapy and to assess the presence/absence of genomic instability using tumor tissue obtained after pathological diagnosis. By clarifying whether genomic instability accurately reflects the efficacy of immunotherapy in urothelial carcinoma, we will evaluate its potential as useful biomarkers for determining whether to continue or modify treatment. Furthermore, we will explore its potential utility as clinical information that could contribute to the development of novel therapeutic agents.
Methods: Whole exome sequencing, RNA sequencing, Whole genome sequencing, single-cell RNA sequencing, spatial transcriptomics (Visium)
Participants/Materials: One patient diagnosed with urothelial carcinoma who received immunotherapy. Tumor tissues were obtained from either 8 organs (primary lesion, peritumoral region, retroperitoneal lymph nodes, two distinct para-aortic lymph nodes, cervical lymph nodes, right lung metastasis, and left lung metastasis) or 5 organs (central region of the primary tumor, retroperitoneal lymph nodes, para-aortic lymph nodes, cervical lymph nodes, and left lung metastasis).
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000725 | Controlled-access (Type I) | 2025/07/08 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
Urothelial carcinoma (ICD10: C679): 1 case tumor tissues: 58 samples from 8 organs |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | DNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| 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 | JGAD000858 |
| Total Data Volume | 4.8 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Urothelial carcinoma (ICD10: C679): 1 case tumor tissues: 58 samples from 8 organs |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA Exome kit |
| Fragmentation Methods | chemical fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000858 |
| Total Data Volume | 4.8 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Urothelial carcinoma (ICD10: C679): 1 case tumor tissues: 8 samples from 8 organs |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | DNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT REAGENT KIT + Human Agilent V6 |
| 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 | JGAD000858 |
| Total Data Volume | 4.8 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Urothelial carcinoma (ICD10: C679): 1 case tumor tissues: 5 samples from 5 organs |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Fixed RNA Profiling |
| Fragmentation Methods | included in the above protocol |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 118 bp |
| Mapping Methods | Cell Ranger v9.0.0 |
| Mapping Quality |
Reads mapped to probe set: 97.2% Reads confidently mapped to probe set: 96.2% Reads confidently mapped to filtered probe set: 93.8% Reads half-mapped to probe set: 0.5% Reads split-mapped to probe set: 0.5% |
| Reference Genome Sequence | refdata-gex-GRCh38-2024-A (GENCODE v44) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000858 |
| Total Data Volume | 188.1 GB (bam) |
| Comments (Policies) | NBDC policy |
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
Urothelial carcinoma (ICD10: C679): 1 case tumor tissues: 7 samples from 5 organs |
| Targets | Visium Spatial Gene Expression, Histological image |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | tumor samples from surgically resected tissues |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression for FFPE, human transcriptome probe kit/Visium CytAssist Spatial Gene Expression for FFPE, human transcriptome probe kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 78 bp |
| Software | Space Ranger v1.3.1, v3.1.2 |
| Reference | refdata-gex-GRCh38-2020-A (GENCODE v32) |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000858 |
| Total Data Volume | 188.1 GB（fastq, tif, xlsx) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Nobuyuki Tanaka
Affiliation: Department of Urology, Keio University School of Medicine
Project / Group Name:
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Prognostic modeling of myxoid liposarcoma by gene expression and histopathology with focus on tumor immunity | 20K16408 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | Identification of Treatment-Related Factors Using Multi-Region Analysis Before and After Cancer Immunotherapy | 22K15576 |
| KAKENHI Scientific Research (C) | Elucidation of the role of long non-coding RNA in bladder cancer | 23K08724 |
| KAKENHI Grant-in-Aid for Challenging Research (Exploratory) | Establishment of a research platform for visualization of tumor heterogeneity and clinical application | 21K19414 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | In situ analysis of diverse urothelial carcinoma immunogenomics and liquid biopsy study | 22H03217 23K24476 |
| KAKENHI Grant-in-Aid for Challenging Research (Pioneering) | Spatial Analysis of Stromal Trajectory Map and Establishment of New Stromal Reprogramming Method under Cancer Immunotherapy | 24K21301 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Clonal Evolution of Urologic Cancer and Spatial Analysis of Tumor Stroma to Elucidate Immunotherapy Resistance Mechanisms | 24H00649 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Integrated Multi-Omics Analysis Methodology with Image Transformation and Deep Learning for Pathophysiology and Drug Response Mechanisms | 20H03240 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Embed omics data to quantum computation and construct predictive models with quantum-classical hybrid machine learning | 25K02261 |
| Moonshot R&D Program, Japan Science and Technology Agency (JST) | Realization of a society watched over by remote control of intracellular cybernetic avatars | JPMJMS2217 |
| Core Research and Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST) | Development of AI-driven single molecule nanopore measurement methods from biological environments | JPMJCR2231 |
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 |
|---|---|---|---|---|---|
