Table 2.

Main genomic characteristics predicting outcome in HGT1 bladder cancer.

	Good outcome	Recurrent	Progression	Microstaging pT1b (deeper level of invasion)
TMB	High	Low	Intermediate
Mutation frequency analysis	ERCC2 (P#< 0.003, q = 0.1)	RHOB and ARID1A (q > 0.1, P# < 0.05)	TP53, ATM, ARID1A, AHR, SMARCB1 (q > 0.1, P# < 0.05)
	BRCA2 (P# < 0.05) but q > 0.1
	Mutations in DDR genes (P = 0.007)
Mutational signature analysis	COSMIC2 (C>T mutations at TCW; P = 0.047)
	COSMIC 5 in ERCC2 mutants (P = 0.0002)
MSig clustering	MSig3 (associated with ERCC2 mutations and COSMIC5; 7/7 GO; P = 0.13)	MSig1 (P = 0.04)	MSig4 with high APOBEC activity and TP53 mutations (3/6 PD)	MSig4 (highest APOBEC with TP53 mut; 5/6 pT1b)
CN alterations		Focal PVRL4 amplification (P = 0.08) CDKN2A deletion (PD&R, P = 0.04) Focal CCNE1 amplification (PD&R, P = 0.04)
MutCN clusters	MutCN2 in 73% of GO (P = 0.04)	MutCN1 cluster-enrich (PD&R, P = 0.04)		MutCN1 clustering has 89% of pT1b samples (P = 0.05; TP53, E2F3.amp, CCNE1.amp, other focal CN events)

Note: P#, empirical P value from the random permutation method correcting for heterogeneous mutation burdens among different outcome groups.