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 IDType of DataCriteriaRelease Date
JGAS000622 NGS (Target Capture) Controlled-access (Type I) 2023/07/27

*Release Note

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JGAS000622

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):

NameTitleProject 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

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