NBDC Research ID: hum0531.v2
SUMMARY
Aims: Urological malignancies, including prostate, kidney, and bladder cancers, are increasing, with somatic genomic alterations playing a key role. Traditional analyses are insufficient to fully explain tumorigenesis. Using next-generation sequencing, this study aims to comprehensively identify tumor-specific alterations and novel therapeutic targets through multi-layered genomic analysis.
Methods: Targeted panel analysis using the NOIR-SS method was performed on formalin-fixed paraffin-embedded (FFPE) tumor tissues from 15 patients with advanced urothelial carcinoma and identified somatic mutations. Plasma cfDNA (50 samples) from the same patients was analyzed using a tumor-informed approach, focusing on the mutations identified in the corresponding tumor tissues. We performed exome sequencing (exome-seq) using the Twist platform on 125 tumor samples obtained from 54 patients with renal cell carcinoma, along with corresponding normal samples. RNA sequencing (RNA-seq) was conducted using the NEB platform on 91 tumor samples from 91 patients with renal cell carcinoma. Furthermore, single-cell RNA sequencing (scRNA-seq) was performed using the 10x Genomics platform on 24 tumor samples obtained from 18 patients with renal cell carcinoma. Spatial transcriptomic analysis was also carried out using the 10x Genomics platform on 26 tumor samples from 16 patients with renal cell carcinoma.
Participants/Materials: Advanced urothelial carcinoma 15 cases, renal cancer 101 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000836 | NGS (Amplicon-seq) | Controlled-access (Type I) | 2025/11/11 |
| JGAS000855 | Controlled-access (Type I) | 2025/11/13 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
advanced urothelial carcinoma (ICD10: C67, C65, C66): 15 cases tumor tissues (FFPE): 15 samples cfDNA (plasma): 50 samples |
| Targets | Amplicon-seq |
| Target Loci for Capture Methods | TP53, FGFR3, TERT, KRAS/HRAS |
| Platform | Thermo Fisher Scientific [Ion PGM/S5] |
| Library Source | DNAs extracted from tumor tissues and cfDNA |
| Cell Lines | - |
| Library Construction (kit name) | Based on the method described by Kukita Y et al. (PLOS ONE, 2018) |
| Fragmentation Methods |
FFPE: Ultrasonic fragmentation (Covaris) plasma cfDNA: - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000978 |
| Total Data Volume | 7.2 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
renal cancer (ICD10: C64): 54 cases tumor tissues: 125 samples non-tumor tissues (cyst): 36 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Twist Library Preparation Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | BWA-MEM |
| Mapping Quality | MAPQ > 20 |
| Reference Genome Sequence | GRCh38 |
| Coverage (Depth) | 127x |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000997 |
| Total Data Volume | 1.0 TB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
renal cancer (ICD10: C64): 91 cases tumor tissues: 91 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000997 |
| Total Data Volume | 1.0 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
renal cancer (ICD10: C64): 18 cases tumor tissues: 24 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Single Cell 3’ Reagent Kit V3.1 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 28 bp + 90 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000997 |
| Total Data Volume | 1.0 TB (barcodes.tsv, features.tsv, matrix.mtx) |
| Comments (Policies) | NBDC policy |
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
renal cancer (ICD10: C64): 16 cases tumor tissues: 22 samples |
| Targets | Visium Spatial Gene Expression, Histological image |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Novaseq 6000] |
| Library Source | tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression library preparation slide |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 28 bp + 50 bp |
| Software | Space Ranger Pipeline (version 1.3.1) |
| Reference | GRCh38 |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000997 |
| Total Data Volume | 1.0 TB (h5) |
| Comments (Policies) | NBDC policy |
Xenium In Situ Gene Expression
| Participants/Materials |
renal cancer (ICD10: C64): 3 cases tumor tissues: 4 samples |
| Targets | Xenium In Situ Gene Expression |
| Target Loci for Capture Methods | - |
| Platform | 10x Genomics [Xenium] |
| Source | tumor tissues |
| Cell Lines | - |
| Reagents (Panel, Kit, Version) | Xenium In Situ Gene Expression, Xenium Human Multi-Tissue and Cancer Panel |
| Software | Xenium Analyzer |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000997 |
| Total Data Volume | 1.0 TB (h5, tif, parquet) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yoichi Fujii
Affiliation: Department of Urology, The University of Tokyo Graduate School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Quantification of ctDNA and Identification of Background Factors in Clear Cell Renal Cell Carcinoma Using NOIR-SS | 23K08731 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Spatial analyses of kidney cancer in hemodialysis patients for innovative screening strategy | 24ck0106948 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | High Sensitivity ctDNA Analysis Using a Novel Panel and NOIR-SS Technology for Monitoring Advanced Urothelial Carcinoma | JGAD000978 | |
| 2 | Spatial multiomic analyses reveal carcinogenic pathways in end-stage renal disease, Cancer Discovery 2025 | JGAD000997 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
