REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Fresh frozen tissue samples	Leeds Multidisciplinary Research Tissue Bank	N/A
Venous blood samples from bladder cancer patients	Leeds Multidisciplinary Research Tissue Bank	N/A
Critical Commercial Assays
Affymetrix GeneChip Human Transcriptome Array 2.0 and Genechip WT PLUS Reagent Kit	Affymetrix	Cat# 902310
GeneChip Hybridization, Wash, and Stain Kit	Affymetrix	Cat# 900720
Gentra Puregene Tissue Kit	QIAGEN	Cat# 158667
HiSeq 3000	Illumina	N/A
NEBNext DNA Library Prep Master Mix Set for Illumina	New England BioLabs	Cat# E6040L
NEBNext Singleplex Oligos for Illumina	New England BioLabs	Cat# E7350L
NEBNext High-Fidelity 2X PCR Master Mix	New England BioLabs	Cat# M0541L
QIAamp DNA Mini Kit	QIAGEN	Cat# 51306
RNeasy Plus Micro Kit	QIAGEN	Cat# 74034
SureSelectXT Human All Exon v6 Kit	Agilent Technologies, Inc	Cat# 5190-8864
Deposited Data
Raw and processed Affymetrix microarray data	This study	GSE:163209
Whole exome sequence data	This study	EGAS00001005765
Targeted sequence data	This study	EGAS00001005766, EGAS00001005767
Software and algorithms
Affymetrix Expression Console software	Affymetrix	https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html
GenePattern	Broad Institute	https://cloud.genepattern.org
GSEA	Subramanian et al.78	https://www.gsea-msigdb.org/gsea/
Nexus Copy Number	Biodiscovery, Inc	http://www.biodiscovery.com/nexus-copy-number
ngCGH	Gartner et al.79	https://github.com/seandavi/ngCGH
R version 3.6.1	The R Foundation for Statistical Computing	https://www.r-project.org/
R studio for Mac	R-Studio	https://www.rstudio.com/products/rstudio/download/
R2	Jan Koster, Academic Medical Center, Netherlands	R2: Genomics Analysis and visualization Platform; https://hgserver1.amc.nl:443/
dNdScv	Martincorena et al., 201737	https://github.com/im3sanger/dndscv
MutationalPatterns	Blokzijl et al., 201880	https://bioconductor.org/packages/release/bioc/html/MutationalPatterns.html
ESTIMATE	Yoshihara et al.30	https://bioinformatics.mdanderson.org/public-software/estimate/
COSMIC mutational signatures v3	N/A	https://cancer.sanger.ac.uk/signatures/
FASTQC	The Babraham Bioinformatics group	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Cutadapt	Marcel Martin 2011	https://github.com/marcelm/cutadapt/
BWA	Li et al.81	https://github.com/lh3/bwa
Picard	Broad Institute	https://broadinstitute.github.io/picard/
GATK3	Broad Institute	https://accounts.google.com/ServiceLogin?service=cloudconsole&passive=1209600&osid=1&continue=https://console.cloud.google.com/storage/browser/_details/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2&followup=https://console.cloud.google.com/storage/browser/_details/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2
ContEst	Broad Institute	http://software.broadinstitute.org/cancer/cga/contest
Conpair	Bergmann et al.82	https://github.com/nygenome/Conpair
samtools	Li et al., 200983	http://samtools.sourceforge.net/
MuTect2	Benjamin et al.84	https://accounts.google.com/ServiceLogin?service=cloudconsole&passive=1209600&osid=1&continue=https://console.cloud.google.com/storage/browser/_details/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2&followup=https://console.cloud.google.com/storage/browser/_details/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2
MuSE	Fan et al.85	https://bioinformatics.mdanderson.org/public-software/muse/
VarScan 2	Koboldt et al.86	http://massgenomics.org/varscan
Strelka2	Kim et al.87	https://github.com/Illumina/strelka
EBCall	Shiraishi et al.88	https://github.com/friend1ws/EBCall
MeerKat	CBMI, Harvard Medical School	http://compbio.med.harvard.edu/Meerkat/
coxph	Therneau (2021). A Package for Survival Analysis in R. R package version 3.2-13.	https://cran.r-project.org/web/packages/survival/index.html
coxphw	Dunkler et al.89	N/A
RTN	Castro et al.25	http://www.bioconductor.org/packages/release/bioc/html/RTN.html