MLPA analysis of amplification in bladder cancer cell lines.

<p>Genomic copy number is shown only when values are ≥4.0. bladder cancer cell lines had no amplification and are not listed above: J82, 639V, MGH-U1, MGH-U3, MGH-U4, MGH-U5, RT4, T24, 253J, 647V, UMUC15, BL17, UMUC3, UMUC6, HCV29, 97–1.</p

Chromosomal regions and genes analyzed by MLPA.

<p>Chromosomal regions and genes analyzed by MLPA.</p

Mutations in the discovery cohort of 80 urothelial carcinoma samples identified by MIP analysis and validated by Sanger sequencing.

1<p>Number of different samples with this mutation.</p>2<p>Stage of the urothelial carcinoma samples with mutation.</p

Identification of nine genomic regions with high level amplification seen in at least 3 of 73 urothelial carcinoma samples in the discovery cohort by MIP analysis.

*<p>copy number values of the 3 urothelial carcinoma samples with the largest amplification of the region (largest to smallest).</p

Summary of MLPA findings in FFPE bladder cancer samples according to stage.

<p>Groups 1, 2, and 3 have a statistically significant difference in the frequency of any amplification event, with p = 0.0020 comparing groups 1 and 2, and p = 0.0011 comparing groups 1 and 3. P is not significant comparing group 2 with group 3. Fisher exact test.</p

MLPA analysis of amplification in the validation cohort of 84 bladder cancer FFPE samples.

<p>Genomic copy number is shown only when values were ≥4.0.</p><p>51 samples are not listed, as they had no amplification events detected (all CN<4.0). The stage and grade distribution of these samples was: 13 Ta grade 1; 8 Ta grade 1–2; 9 Ta grade 3; 21 T2 grade 3.</p

GISTIC plot of genomic regions with CN gain or loss from the MIP analysis on 73 urothelial carcinoma specimens.

<p>The 21 autosomes are shown on the y axis, and q values indicating statistical significance from the GISTIC analysis are plotted on the x axis for regions of copy number gain (red at left) and loss (blue at right).</p