Biomarker analysis
death, tumor, ®, tumors, PD‐L1
BLOOD, TUMOR, TUMORS, DNA DAMAGE
Tissue samples obtained from patients during TURBT and peripheral blood samples were collected for assessing programmed cell death ligand 1 (PD‐L1) expression and WES prior to treatment. PD‐L1 expression was evaluated with the IHC 22C3 pharmaDx (Agilent Technologies). DNA was extracted from TURBT tissue and peripheral blood samples, and invasive tumor content was assessed by pathologists to ensure sufficient tumor cells. DNA was extracted using the DNeasy Blood and Tissue Kit (69,504, QIAGEN). Targeted capture pulldown and exon‐wide libraries were created from native DNA using NadPrep® Hybrid Capture Reagents (for Illumina®, 1,005,101) and NadPrep® DNA Library Preparation Kit (for Illumina®, 1,002,103) E96. Paired‐end sequence data were generated using Illumina NovaSeq machines with an average sequencing depth of 100 × for controls and 200 × for tumors.The DNA damage response and repair (DDR) gene set, consisting of 276 genes, was built by assembling relevant gene lists, including MSigDB v5.0 (an online catalog of DDR genes from recently published resources), and knowledge‐based curation of information on specific DNA repair pathways or sub‐pathways, as previously reported.