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 |