NBDC Research ID: hum0460.v1
SUMMARY
Aims: Preliminary analysis was conducted to develop a cfDNA-based platform capable of predicting gene mutation profiles, TMB, gene expression profiles (molecular subtype diagnosis), and immunohistochemical findings (PD-L1 expression) using the primary lesion tissue of bladder cancer and upper urinary tract epithelial cancer, verifying the feasibility of such development.
Methods: Target capture sequencing, RNA sequencing
Participants/Materials: advanced urothelial carcinoma (bladder cancer, upper urinary tract epithelial cancer) : 82 cases
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000714 | NGS (Target Capture, RNA-seq) | Controlled-access (Type I) | 2025/01/29 |
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MOLECULAR DATA
| Participants/Materials |
advanced urothelial carcinoma (ICD10: C66, C67): 82 cases plasma cfDNA: 158 samples tumor tissues: 73 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods |
53 UC-relevant genes and TERT promoter AKT1, AKT2, AKT3, ARID1A, ASXL2, ATM, BRAF, CCND1, CCND2, CCND3, CCNE1, CDK4, CDK6, CDKN1A, CDKN2A, CREBBP, E2F3, EGFR, ELF3, EP300, ERBB2, ERBB3, ERCC2, FAT1, FBXW7, FGFR1, FGFR3, JAK1, JAK2, KDM6A, KMT2A, KMT2C, KMT2D, MAP2K4, MDM2, NF1, PBRM1, PIK3A, PPARG, PTEN, RAC1, RAF1, RAS, RB1, SPTAN1, STAG2, TERT, TP53, TSC1, TSC2, MLH1, MSH2, MSH6, PMS2 |
| Platform | Illumina [NovaSeq 6000, HiSeq X] |
| Library Source | plasma cfDNA and DNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SMARTer ThruPLEX tag-seq Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Software | eVIDENCE pipline |
| Mapping Methods | eVIDENCE pipline |
| Mapping Quality | - |
| Reference Genome Sequence | GRCh37 |
| Coverage (Depth) | 1086 |
| Detecting Methods for Variation | eVIDENCE pipline |
| Variant Numbers (after QC) | 683 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000847 |
| Total Data Volume | 282.6 GB (bam, csv, tab) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
advanced urothelial carcinoma (ICD10: C66, C67): 82 cases tumor tissues: 68 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) | TruSeq Stranded mRNA Sample Prep Kit |
| Fragmentation Methods | Exposure to divalent cations at elevated temperatures |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Software | Genomon 2.6.3 |
| Mapping Methods | Genomon 2.6.3 |
| Mapping Quality | - |
| Reference Genome Sequence | GRCh37 |
| QC | Genomon 2.6.3 |
| Gene Number | based on Genomon 2.6.3 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000847 |
| Total Data Volume | 282.6 GB (bam, csv, tab) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takashi Kobayashi
Affiliation: Department of Urology, Kyoto University Graduate School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Chugai Pharmaceutical Co., Ltd. | Pilot study towards the development of a Companion/Complimentary Diagnosis platform using liquid biopsy with cfDNA for immune checkpoint inhibitor therapy in advanced urothelial cancer | R2636 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Clinical Utility of Serial Circulating Tumor DNA Analysis as a Minimally Invasive Biomarker in Advanced Urothelial Cancer | doi: 10.1200/PO-24-00472 | JGAD000847 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
