NBDC Research ID: hum0531.v1
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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.
Participants/Materials: Advanced urothelial carcinoma 15 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000836 | NGS (Amplicon-seq) | Controlled-access (Type I) | 2025/11/11 |
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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 |
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 |
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 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
