NBDC Research ID: hum0403.v1
SUMMARY
Aims: To prospectively identify new biomarkers by evaluating gene mutations and microRNA expression using tumor tissues and free nucleic acids collected from patients with urologic cancer.
Methods: Cell-free DNAs extracted from plasma samples were subjected to a circulating tumor DNA analysis using the AVENIO ctDNA Expanded Kit (Roche Diagnostics, Basel, Switzerland). DNA concentration was assessed using a Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA).
Participants/Materials: 16 plasma samples were collected before immune checkpoint inhibitor treatment and 9 plasma samples were collected after immune checkpoint inhibitor treatment from 16 metastatic urothelial carcinoma patients.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000622 | NGS (Target Capture) | Controlled-access (Type I) | 2023/07/27 |
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| Participants/Materials |
metastatic urothelial carcinoma (ICD10: C65, C66, C67.9): 16 cases 16 plasma samples collected before immune checkpoint inhibitor treatment 9 plasma samples collected after immune checkpoint inhibitor treatment |
| Targets | Target Capture |
| Target Loci for Capture Methods | 77 genes |
| Platform | Illumina [NextSeq 500] |
| Library Source | cell-free DNA in plasma |
| Cell Lines | - |
| Library Construction (kit name) | AVENIO ctDNA Expanded Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp x 2 |
| Mapping Methods | AVENIO ctDNA Analysis Software Version 2.0.0 |
| Mapping Quality | 99.99997595 |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | 7243 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000751 |
| Total Data Volume | 40.8 GB (bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kazuki Hamada
Affiliation: Department of Urology, University of Tsukuba Hospital
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Application of whole blood RNA in urological cancer to understand immune cell diversity and predict therapeutic effect | 21K09365 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Variant allele frequency changes in TP53 predict pembrolizumab response in patients with metastatic urothelial carcinoma. | doi: 10.3892/ol.2023.13975 | JGAD000751 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
