1. Clinical characteristics of 37 bladder cancer patients. Patient ID Patient age (years) Sex Stage (TNM classifcation*) Grade Primary/Recurrent B105 M T2N0M0 high Recurrent B65 M T3aN0M0 high Recurrent 
* The TNM cancer staging system was designed to gauge the extent of cancer in a patient's body. T describes the size of the tumor and whether it has invaded nearby tissue, N describes regional lymph nodes that are involved, and M describes distant metastasis (spread of cancer from one body part to another). 


Table 4 . The detailed information of somatic SNV and INDEL validation.

 4 
	B80-1	M	T2N0M0	high	Recurrent
	B98	M	T3N1M0	low	Recurrent
	B109	M	TaN0M0	low	Recurrent
	B11	M	T4N0M0	high	Recurrent
	B25	M	T4aN0M0	high	Recurrent
	B71	M	T2N0M0	low	Recurrent
	B96	M	T3N0M0	high	Recurrent
	B73	M	TaN0M0	low	Recurrent
	B80-5	M	TaN0M0	low	Recurrent
	B112	M	TaN0M0	low	Recurrent
	W67	M	T1N0M0	low	Recurrent
	W68	M	T1N0M0	high	Recurrent
	W70	F	T1N0M0	high	Recurrent
	W72	M	T1N0M0	high	Recurrent
	chencian	M	T3bN0M0	high	Recurrent
	B57	F	T2aN0M0	low	Primary
	B59-3	M	T2N0M0	low	Primary
	B68	M	T2N0M0	low	Primary
	B64	M	TaN0M0	low	Primary
	B66-0	F	TaN0M0	high	Primary
	B78	M	TaN0M0	low	Primary
	B89-10	M	TaN0M0	high	Primary
	B21	M	T2N0M0	low	Primary
	B70	M	T2N0M0	high	Primary
	B80-0	M	TaN0M0	low	Primary
	B80-13	M	TaN0M0	high	Primary
	B59-0	M	T2N0M0	low	Primary
	B59-1	M	T1N0M0	low	Primary
	B45	M	TaN0M0	high	Primary
	B56	M	TaN0M0	low	Primary
	B62-0	M	TaN0M0	high	Primary
	B80-11	M	TaN0M0	low	Primary
	B89-5	M	TaN0M0	high	Primary
	B99	F	T3N0M0	low	Primary
	B77	M	T1N0M0	high	Primary

* SR, supplementary relapsed tumor. SP, supplementary primary tumor. The TNM cancer staging system was designed to gauge the extent of cancer in a patient's body. T describes the size of the tumor and whether it has invaded nearby tissue, N describes regional lymph nodes that are involved, and M describes distant metastasis (spread of cancer from one body part to another). 
Table 7 . PCR primer sequences for selected genes.

 7 
	Gene	Forward primer	Reverse primer	RT-PCR
	ACTB	GTCACCAACTGGGACGACAT	AGGGATAGCACAGCCTGGAT	RT-PCR
	MLL	AAAGCCCTCGAAGGATTAAG	AGCACTGACAACAGGCATGAT	RT-PCR
	EP400	GAAGCACAGTAGAGACGGACC	CTGGAAAACTACCCCTTGGTG	RT-PCR
	PRDM2	GGGCCATTTGTTGGTGATAAGA	AAGCCCAATTCACATATCGCA	RT-PCR
	TMPRSS13	GGCTGCGTGAGGTTTGACT	TCCGGTGAGCACTCTCGAA	RT-PCR
	GATA4	GTGTCCCAGACGTTCTCAGTC	GGGAGACGCATAGCCTTGT	RT-PCR
	GATA6	CTCAGTTCCTACGCTTCGCAT	GTCGAGGTCAGTGAACAGCA	RT-PCR
	MMP2	GATACCCCTTTGACGGTAAGGA	CCTTCTCCCAAGGTCCATAGC	RT-PCR
	MMP13	CCAGACTTCACGATGGCATTG	GGCATCTCCTCCATAATTTGGC	RT-PCR
	ETS1	TACACAGGCAGTGGACCAATC	CCCCGCTGTCTTGTGGATG	RT-PCR
	HOXA9	GTCCAAGGCGACGGTGTTT	CCGACAGCGGTTCAGGTTTA	RT-PCR
	GATA4	CTGGGTAGGGGCTGGAGTAG	CTGGCCGAGAGCAGTACG	CHIP
	ETS1	CTGGGCTCGGTGAGGAACGCCCT	AGTCCGCGCGAAGTTGGCACTT	CHIP
	MLL (g.chr11:118359433)	AAGAAGGGTATGGTTGATTATGTT	AGCTGTAGTTCTATTACCAAGTTT	DNA-PCR
	MLL (g.chr11:118375263)	TACCCCCTCCGACAAAAATTTACT	GTGATGGTTACTCTCTTCTCCCCT	DNA-PCR
	MLL (g.chr11:118359433)	GTTTATGGATGAGGTTTTGACTCC	ATGAGGTATTATTGGGGCTTGGTT	DNA-PCR
	MLL (g.chr11:118359433)	GAGTACCAATTAAAACCAGGTTTG	TCCTGATGTATCTCTGCAACAAAC	DNA-PCR

Supplementary Table

 2. Summary statistics of exome sequencing data obtained from the 20 primary bladder cancer patients. 

Supplementary