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 IDType of DataCriteriaRelease Date
JGAS000725

NGS (Exome)

NGS (RNA-seq)

NGS (WGS)

NGS (scRNA-seq)

NGS (Visium Spatial Gene Expression), Histological image

Controlled-access (Type I) 2025/07/08

*Release Note

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MOLECULAR DATA

Exome

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

 

RNA-seq

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

 

WGS

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

 

scRNA-seq

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):

NameTitleProject 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

TitleDOIDataset ID
1
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use