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Table 3 Focal gene copy number alterations and minimal common regions (MCR) identified using waviCGH in UBC lines

From: The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies

Variation type Chr Length (KB) Number of probes Adjusted p value Frequency (% Cell Lines) CytoBand (Probe boundaries) Number of genes Previously described
GAIN 1 15995 4751 0.05 35 1q25.3-1q31.3 (rs502870- rs590258) 164 Tumors: 1q gain, 1q24.2 and 1q23 amplification SETDB1 (1q21)
1 1517 695 0.05 38 1q32.2 (rs1126573- rs2494606) 0 Novel
3 4084 1623 0.02 35 3q21.3-3q22.1 (rs34267791-rs6439205) 110 3q21.3 tumors
5 49651 16712 0.05 35 5p13.1-5p12 (rs28538767- rs36047540) 609 Novel
7 55653 22123 0.01 42 7p15.2-7p11.2 (rs4096522- rs10280445) 848 7p11.2 amplification high grade tumors
7 840 347 0.05 38 7q11.23 (rs11544049- rs2074666) 22 Novel
7 21068 7166 0.05 38 7q21.3-7q31.2 (rs10953601- rs10246291) 847 7q22.1 and 7q32 amplification in tumors
7 3252 1290
7 24003 7258
7 211 96 0.05 38 7q33 (rs10260266- rs3807337) 5 Novel
11 3044 1510 0.05 35 11p15.5-11p15.4 (rs4029252- rs7103275) 152 Tumors: 11p loss
LOSS 3 22040 8521 0.04 46 3p21.1-3p14.2 (rs4927997- rs13075591) 240 Tumors/cell lines
4 310 78 0.01 44 4p16.3 (rs10446889- rs13137548) 15 Tumors/cell lines
4 665 272 0.05 40 4p16.3-4p15.1 (rs1728273- rs11930062) 379 Tumors/cell lines
4 4561 2058
4 22491 7467
4 1839 399 0.05 40 4p13-4q35 (rs7665332- rs13124496) 2003 Tumors/cell lines
4 155726 47697 0.01 44
6 4227 3338 0.01 42 6p22.1 (rs498548- rs9468692) 267 MHC region
10 640 424 0.03 40 10q23.33 (rs17110194- rs11188277) 17 Tumors/cell lines
13 1.60 5 0.03 38 13q33.3 (rs3093749- rs1805385) 1 Tumors/cell lines
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