Table 2 Frequency of amplifications and deletions in a focused analysis of 32 genomic regions which were either previously known to be of interest in urothelial cancer or which were identified by TCGA as having statistically significant focal copy number changes

MAP kinase pathway

ERBB2^

2/29-7%

4/30-13%

FGFR3^

0/29-0%

1/30-3%

FGFR1^

2/29-7%

4/30-13%

EGFR^

0/29-0%

0/30-0%

MET^

0/29-0%

0/30-0%

KRAS^

0/29-0%

0/30-0%

NF1^

0/29-0%

1/30-3%

BRAF^

0/29-0%

0/30-0%

RAF1^

1/29-3%

3/30-10%

MYC^

0/29-0%

2/30-7%

MYCL1^

5/29-17%

3/30-10%

P53 pathway

MDM2^

1/29-3%

3/30-10%

TP53 ^∨

2/29-7%

2/30-7%

RB pathway*

CDKN2A ^∨

8/29-28%

10/30-33%

CDK4 ^

1/29-3%

2/30-7%

CCND1 ^

2/29-7%

6/30-20%

CCNE1^

2/29-7%

4/30-13%

RB1 ^∨

0/29-0%

2/30-7%

E2F3^ *(p = 0.04)

2/29-7%

9/30-30%

PI3K pathway

PTEN ^∨

1/29-3%

1/30-3%

PIK3CA^

0/29-0%

0/30-0%

AKT1^

0/29-0%

1/30-3%

TSC1 ^∨

1/29-3%

1/30-3%

MTOR^

0/29-0%

0/30-0%

Others

BCL2L1^

1/29-3%

1/30-3%

PPARG^

1/29-3%

5/30-17%

CREBBP ^∨

0/29-0%

1/30-3%

PVRL4^

2/29-7%

7/30-23%

YWHAZ^

5/29-17%

4/30-13%

NCOR1 ^∨

2/29-7%

1/30-3%

YAP1^

0/29-0%

1/30-3%

ZNF703^

1/29-3%

3/30-10%

n = 928

n = 960

% total loci with amplification/deletion*

(p < 0.001)

42/928-4.5%

83/960-8.6%