Unique Name	Descriptor	Wide Peak Limits	Peak Limits	Region Limits	q values	Residual q values after removing segments shared with higher peaks	Broad or Focal	Amplitude Threshold	TCGA-D3-A2JA-06A-11D-A194-01	TCGA-D3-A2JF-06A-11D-A194-01	TCGA-DA-A1I0-06A-11D-A20B-01	TCGA-DA-A1IC-06A-11D-A191-01	TCGA-EE-A17X-06A-11D-A191-01	TCGA-EE-A180-06A-11D-A219-01	TCGA-EE-A181-06A-11D-A194-01	TCGA-EE-A182-06A-11D-A194-01	TCGA-EE-A20C-06A-11D-A194-01	TCGA-EE-A29L-06A-12D-A194-01	TCGA-EE-A29N-06A-12D-A191-01	TCGA-EE-A29V-06A-12D-A191-01	TCGA-EE-A2A2-06A-11D-A194-01	TCGA-EE-A2GC-06A-11D-A191-01	TCGA-EE-A2GO-06A-11D-A194-01	TCGA-EE-A2GR-06A-11D-A191-01	TCGA-EE-A2MI-06A-11D-A191-01	TCGA-EE-A2MJ-06A-11D-A191-01	TCGA-EE-A2MS-06A-11D-A191-01	TCGA-EE-A2MT-06A-11D-A191-01	TCGA-EE-A3AE-06A-11D-A194-01	TCGA-EE-A3J5-06A-11D-A20B-01	TCGA-EE-A3JD-06A-11D-A20B-01	TCGA-ER-A19A-06A-21D-A191-01	TCGA-ER-A19F-06A-11D-A194-01	TCGA-FS-A1Z3-06A-11D-A191-01	TCGA-FS-A1ZA-06A-11D-A191-01	TCGA-FS-A1ZP-06A-11D-A191-01	TCGA-FS-A1ZZ-06A-11D-A191-01	TCGA-FW-A3I3-06A-11D-A219-01	TCGA-GN-A266-06A-11D-A191-01	
Amplification Peak 1	1p12   	chr1:119797140-149881397(probes 67344:67832)    	chr1:119797211-120521759(probes 67345:67826)  	chr1:117947365-149885582(probes 66340:67835)  	0.00014685	 0.00014685		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	1	0	0	0	0	2	1	0	0	2	0	2	0	0	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	1	1	
Amplification Peak 2	1q44   	chr1:226892109-249250621(probes 115805:129201)  	chr1:247386826-247492646(probes 128933:129003)	chr1:242663196-249250621(probes 126720:129201)	0.099401	   0.099401		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	1	0	1	2	0	2	1	2	0	2	0	0	1	0	1	0	0	1	1	2	0	0	0	0	1	1	1	2	2	1	1	
Amplification Peak 3	7p22.3 	chr7:1-49161068(probes 666873:695220)               	chr7:911508-1388674(probes 666952:666994)          	chr7:1-3598281(probes 666873:667968)               	0.22956	    0.22956		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	1	0	1	2	0	1	1	0	0	2	1	0	0	0	1	0	0	1	2	0	1	0	0	0	0	2	1	0	2	1	1	
Amplification Peak 4	7q36.1 	chr7:97232455-159138663(probes 716514:748235)    	chr7:152173582-152205019(probes 745036:745048)	chr7:140835277-159138663(probes 739553:748235)	0.22956	    0.22956		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	1	0	2	2	0	1	1	1	0	1	1	0	0	0	1	0	0	1	2	0	1	1	1	0	0	0	0	1	1	1	1	
Amplification Peak 5	12p12.1	chr12:25237725-26874538(probes 1070176:1071484)  	chr12:25237763-25999919(probes 1070177:1070829)	chr12:25237763-26008695(probes 1070177:1070832)	0.22956	    0.22956		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	2	
Amplification Peak 6	15q26.2	chr15:68436609-102531392(probes 1261472:1280742)	chr15:97898842-98146113(probes 1278504:1278659)	chr15:97898842-98570989(probes 1278504:1278947)	0.22956	    0.22956		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	1	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	0	1	1	0	0	0	1	0	2	0	2	0	
Amplification Peak 7	17q25.3	chr17:45627595-81195210(probes 1339832:1358561)  	chr17:78445307-78588201(probes 1357694:1357785)	chr17:71816927-81195210(probes 1355174:1358561)	0.22956	    0.22956		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	0	1	0	1	0	0	1	1	0	2	1	1	0	1	0	1	1	0	1	1	2	1	0	0	1	0	0	0	0	1	0	
Deletion Peak  1	1p36.31 	chr1:1-9908481(probes 1:3856)                         	chr1:6261872-6581282(probes 1973:2086)                	chr1:1-9420540(probes 1:3666)                         	0.047176	    0.11419		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	1	0	0	1	0	1	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	
Deletion Peak  2	1p13.2  	chr1:101698916-149920615(probes 56910:67840)      	chr1:111827680-111863450(probes 62356:62387)      	chr1:110032434-114282286(probes 61222:63923)      	0.13034	    0.13034		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	1	0	1	0	0	0	0	0	1	0	0	1	0	
Deletion Peak  3	2q37.3  	chr2:233898418-243199373(probes 255284:260562)    	chr2:238705738-241909926(probes 258569:260251)    	chr2:238495844-243199373(probes 258387:260562)    	0.022323	   0.022323		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	1	0	0	1	0	0	1	0	0	0	0	1	0	1	0	1	1	0	0	0	0	0	0	0	0	0	1	1	1	
Deletion Peak  4	3q23    	chr3:94639769-150922637(probes 311912:343117)      	chr3:141194981-141333247(probes 338413:338462)    	chr3:141263696-141273396(probes 338438:338439)    	0.12958	    0.12958		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	
Deletion Peak  5	6q23.2  	chr6:1-171115067(probes 570336:666872)              	chr6:133001478-134500924(probes 644158:645179)    	chr6:133019683-133021381(probes 644174:644175)    	0.24092	    0.25082		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	1	0	0	1	1	0	1	0	1	1	0	1	0	0	0	1	1	0	0	0	0	1	0	1	0	1	1	0	
Deletion Peak  6	9p21.3  	chr9:21555227-22448737(probes 843092:843622)        	chr9:21959052-21977193(probes 843309:843310)        	chr9:19677544-26474475(probes 841671:845989)        	3.4534e-16	 3.4534e-16		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	1	1	0	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	0	0	0	1	1	1	0	0	1	1	
Deletion Peak  7	10p15.1 	chr10:1-5407870(probes 897874:901080)                 	chr10:5084929-5151169(probes 900905:900952)          	chr10:5123270-5130184(probes 900929:900930)          	0.02152	    0.02152		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	1	0	0	0	0	0	1	0	0	1	0	0	1	0	1	1	1	0	1	0	1	1	0	0	0	1	1	0	0	0	1	
Deletion Peak  8	10q24.33	chr10:59063766-135534747(probes 931210:978779)    	chr10:105348251-105619553(probes 959201:959357)  	chr10:105504616-105508644(probes 959280:959281)  	0.19712	    0.19712		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	1	0	0	0	0	0	1	0	0	1	0	0	1	1	1	1	1	0	0	0	1	1	0	0	0	1	1	0	0	1	1	
Deletion Peak  9	11q24.3 	chr11:105874594-135006516(probes 1036998:1056065)	chr11:128326464-128395332(probes 1052268:1052477)	chr11:105936089-135006516(probes 1037034:1056065)	0.002248	   0.002248		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	0	0	0	0	1	1	1	1	1	1	1	0	1	1	1	1	1	1	1	0	0	1	1	1	0	1	1	1	
Deletion Peak 10	13q34   	chr13:95351823-115169878(probes 1174066:1186720)  	chr13:114236241-115169878(probes 1186575:1186720)	chr13:114263720-115169878(probes 1186592:1186720)	0.13034	    0.13034		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	1	1	0	0	0	0	1	0	0	0	1	
Deletion Peak 11	14q23.3 	chr14:50572489-104154469(probes 1202060:1235668)  	chr14:65452241-66970919(probes 1211662:1212493)    	chr14:64985729-67242105(probes 1211302:1212554)    	0.14251	    0.14366		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	1	1	0	0	0	0	1	0	1	0	0	1	1	0	0	0	0	0	1	0	0	1	0	0	0	0	1	0	0	0	0	
Deletion Peak 12	16q12.1 	chr16:31722415-65161093(probes 1294578:1306703)    	chr16:48114144-48186372(probes 1295277:1295318)    	chr16:31850300-50189592(probes 1294638:1296686)    	0.011674	   0.011453		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	0	0	0	1	0	1	1	1	0	0	1	1	0	0	1	1	0	1	1	0	0	0	0	1	1	0	1	0	
Amplification Peak 1 - CN values	1p12   	chr1:119797140-149881397(probes 67344:67832)    	chr1:119797211-120521759(probes 67345:67826)  	chr1:117947365-149885582(probes 66340:67835)  	0.00014685	 0.00014685		Actual Copy Change Given	0.41873	0	-0.22305	0.019643	-0.0089704	3.6569	0.1595	0.008892	0.0015041	1.739	-0.053206	1.9685	0.080767	-0.018012	-0.53439	3.6569	3.6569	0.2369	-0.5214	-0.0055375	-0.56465	0.00458	0.066945	0.02525	0	-0.021251	-0.74534	0.0019418	-0.014366	0.60467	0.49286	
Amplification Peak 2 - CN values	1q44   	chr1:226892109-249250621(probes 115805:129201)  	chr1:247386826-247492646(probes 128933:129003)	chr1:242663196-249250621(probes 126720:129201)	0.099401	   0.099401		Actual Copy Change Given	0.41927	0.012795	0.25006	1.461	0.0015936	3.6369	0.1595	1.5401	0.023913	0.93427	-0.053206	0.019783	0.76239	-0.011958	0.46741	0.0019203	-0.0011979	0.2369	0.57836	1.6245	-0.070536	0.008892	-0.091647	-0.044858	0.84711	0.76849	0.79529	2.0866	1.6774	0.54365	0.33464	
Amplification Peak 3 - CN values	7p22.3 	chr7:1-49161068(probes 666873:695220)               	chr7:911508-1388674(probes 666952:666994)          	chr7:1-3598281(probes 666873:667968)               	0.22956	    0.22956		Actual Copy Change Given	0.72188	-0.015191	0.83431	1.5428	0.01105	0.77868	0.87408	0.026935	-0.47549	1.071	0.41764	0.027357	0.087267	0.040395	0.53942	-0.037919	-0.0025462	0.28921	1.3754	0.00083195	0.51592	-0.0024138	0.092635	0.041034	-0.0084385	3.6569	0.68626	0.024408	0.93305	0.5259	0.49182	
Amplification Peak 4 - CN values	7q36.1 	chr7:97232455-159138663(probes 716514:748235)    	chr7:152173582-152205019(probes 745036:745048)	chr7:140835277-159138663(probes 739553:748235)	0.22956	    0.22956		Actual Copy Change Given	0.76628	-0.0021663	1.3246	1.5042	0	0.75131	0.87408	0.60756	0.015653	0.60738	0.457	0.031295	-0.0064839	0.090501	0.49874	-0.0034529	0.0034687	0.29326	1.2697	0.00083195	0.56679	0.67085	0.27793	0.039337	0.038913	-0.0022354	0.036088	0.81454	0.89693	0.50307	0.10804	
Amplification Peak 5 - CN values	12p12.1	chr12:25237725-26874538(probes 1070176:1071484)  	chr12:25237763-25999919(probes 1070177:1070829)	chr12:25237763-26008695(probes 1070177:1070832)	0.22956	    0.22956		Actual Copy Change Given	0	-0.00013862	0.014274	0	0.0137	0.75547	-0.016429	-0.0013858	-0.45955	-0.015329	0.05908	0.6753	-0.383	0	-0.014923	0.016544	-0.0055375	0.010285	-0.010983	0.35953	-0.14799	0.18374	0.019643	-0.028765	-0.014916	-0.012221	-0.32542	-0.0013858	-0.0029091	-0.005261	3.6569	
Amplification Peak 6 - CN values	15q26.2	chr15:68436609-102531392(probes 1261472:1280742)	chr15:97898842-98146113(probes 1278504:1278659)	chr15:97898842-98570989(probes 1278504:1278947)	0.22956	    0.22956		Actual Copy Change Given	0.30105	0.43915	-0.02151	-0.0094046	-0.0050548	0.77887	-0.41036	-0.0011087	0.017191	-0.41135	-0.011363	-0.01414	0.021485	0.04606	0.43395	-0.0015457	0.023566	0.11844	0.59702	-0.038365	0.5252	0.18268	-0.047395	0.035383	0.010703	0.75834	0.029184	2.8272	-0.0096806	1.0778	-0.43606	
Amplification Peak 7 - CN values	17q25.3	chr17:45627595-81195210(probes 1339832:1358561)  	chr17:78445307-78588201(probes 1357694:1357785)	chr17:71816927-81195210(probes 1355174:1358561)	0.22956	    0.22956		Actual Copy Change Given	-0.079244	0.63244	-0.0023553	0.7057	0.0090996	-0.04782	0.35104	0.17181	-0.0015971	1.6698	0.53555	0.61952	0.033571	0.15733	-0.099145	0.58952	0.57269	0.017824	0.343	0.77445	1.5818	0.71264	-0.055769	-0.0089906	0.77791	0.012795	-0.0049844	0.0086135	-0.011749	0.49441	-0.0099815	
Deletion Peak  1 - CN values	1p36.31 	chr1:1-9908481(probes 1:3856)                         	chr1:6261872-6581282(probes 1973:2086)                	chr1:1-9420540(probes 1:3666)                         	0.047176	    0.11419		Actual Copy Change Given	0.41873	0.030169	-0.22305	-0.048067	-0.0089704	-0.66679	0.1595	-0.62808	0.0029381	0.65461	-0.053206	-0.0095426	0.045871	0.045493	-0.56242	-0.4379	0.0052749	0.10982	-1.1875	-0.044009	-0.068799	0.00458	0.066945	0.02525	0	-0.013677	0	0.0019418	-0.042847	-0.52409	0.44935	
Deletion Peak  2 - CN values	1p13.2  	chr1:101698916-149920615(probes 56910:67840)      	chr1:111827680-111863450(probes 62356:62387)      	chr1:110032434-114282286(probes 61222:63923)      	0.13034	    0.13034		Actual Copy Change Given	0.41873	0	-0.22305	0.019643	-0.0089704	-0.017254	0.1595	0.008892	0.0015041	1.739	-0.053206	0.028481	0.12522	-0.69183	-0.53439	-0.4379	-0.63424	0.2369	-0.5214	-0.0055375	-0.56465	0.00458	0.066945	0.02525	0	-0.021251	-0.74534	0.0019418	-0.014366	-0.5162	0.49286	
Deletion Peak  3 - CN values	2q37.3  	chr2:233898418-243199373(probes 255284:260562)    	chr2:238705738-241909926(probes 258569:260251)    	chr2:238495844-243199373(probes 258387:260562)    	0.022323	   0.022323		Actual Copy Change Given	0.54784	-0.0055375	-0.47247	0.0031663	-0.024328	-1.0361	0.068952	0	-0.46456	0.54718	0.054091	0.017963	0.061673	-0.30633	0.08551	-0.40397	0	-0.10395	-0.76102	0	0.24311	-0.0036011	-0.065769	0	-0.01849	-0.057927	0.053948	0	-1.022	-0.31774	-0.85401	
Deletion Peak  4 - CN values	3q23    	chr3:94639769-150922637(probes 311912:343117)      	chr3:141194981-141333247(probes 338413:338462)    	chr3:141263696-141273396(probes 338438:338439)    	0.12958	    0.12958		Actual Copy Change Given	0.3393	0.40348	0.0043021	0.006009	0.0064554	0.79394	0	0.50359	-0.43859	-0.010232	0.050232	0.024127	0.048385	-0.60143	0.033267	0.057204	-0.0024938	-0.028491	0.076358	0.013911	0.30745	0.10994	0.022164	0.025952	-0.89189	0.0039572	0.087021	0.0029133	0.0011093	-1.1443	-0.020138	
Deletion Peak  5 - CN values	6q23.2  	chr6:1-171115067(probes 570336:666872)              	chr6:133001478-134500924(probes 644158:645179)    	chr6:133019683-133021381(probes 644174:644175)    	0.24092	    0.25082		Actual Copy Change Given	-0.09185	-0.46557	0.018383	-0.78889	0.018803	-0.030813	-0.4086	-0.59585	0	-0.63953	-0.034631	-0.68095	-0.82756	0.016493	-0.55447	0.01833	0.56099	0.019223	-0.5641	-0.9	0.10854	0.10979	0.013779	0.041883	-0.89153	-0.03681	-0.73845	-0.01904	-0.99205	-0.59166	0.20534	
Deletion Peak  6 - CN values	9p21.3  	chr9:21555227-22448737(probes 843092:843622)        	chr9:21959052-21977193(probes 843309:843310)        	chr9:19677544-26474475(probes 841671:845989)        	3.4534e-16	 3.4534e-16		Actual Copy Change Given	0.34238	-0.45624	0	-0.80534	-1.2929	-0.03054	-0.79327	-0.58823	-0.4469	-1.2929	-0.33975	-0.68424	0.020644	-0.68173	-1.2929	-1.2929	-1.2179	-0.091684	-1.0959	-0.0096806	-0.1935	0.024127	-0.056038	-0.042245	-1.2929	-1.2929	-1.2929	-0.0055375	0.0081959	-1.2929	-0.10684	
Deletion Peak  7 - CN values	10p15.1 	chr10:1-5407870(probes 897874:901080)                 	chr10:5084929-5151169(probes 900905:900952)          	chr10:5123270-5130184(probes 900929:900930)          	0.02152	    0.02152		Actual Copy Change Given	-0.13888	0.0060797	-0.0085766	-0.00055444	-0.014421	-0.03245	-0.21156	-0.0019399	0.028548	-0.70268	-0.093931	0	-0.16279	0.034605	-0.56704	-0.25069	-0.65174	-0.042652	-1.1466	-0.041024	-0.38915	-0.14682	0.0049969	-0.0063668	-0.00013862	-0.84464	-0.33237	-0.088242	-0.014503	0.48525	-0.53875	
Deletion Peak  8 - CN values	10q24.33	chr10:59063766-135534747(probes 931210:978779)    	chr10:105348251-105619553(probes 959201:959357)  	chr10:105504616-105508644(probes 959280:959281)  	0.19712	    0.19712		Actual Copy Change Given	-0.44637	-0.0028998	-0.017181	-0.00055444	-0.0051931	-0.03245	-0.31459	-0.0019399	0.0195	-0.66235	-0.093931	0	-0.20235	-0.30763	-0.56704	-0.24754	-0.62684	-0.042652	0.026591	-0.027398	-0.36747	-0.14682	0.0049969	-0.0063668	0.011539	-0.82181	-0.33237	-0.088242	-0.0026322	-0.56803	-0.52573	
Deletion Peak  9 - CN values	11q24.3 	chr11:105874594-135006516(probes 1036998:1056065)	chr11:128326464-128395332(probes 1052268:1052477)	chr11:105936089-135006516(probes 1037034:1056065)	0.002248	   0.002248		Actual Copy Change Given	-0.0010057	-0.46745	-0.076412	-0.027669	0.0045093	-0.075078	0.016425	-0.60022	-0.43154	-0.70019	-0.13482	-0.68843	-0.43359	-0.6852	-0.010578	-0.91636	-0.58461	-0.12082	-1.1294	-0.90555	-0.58728	-0.3936	-0.067458	-0.026304	-0.89871	-0.82277	-0.72817	-0.011749	-0.99736	-0.52072	-0.50898	
Deletion Peak 10 - CN values	13q34   	chr13:95351823-115169878(probes 1174066:1186720)  	chr13:114236241-115169878(probes 1186575:1186720)	chr13:114263720-115169878(probes 1186592:1186720)	0.13034	    0.13034		Actual Copy Change Given	0.33217	0.42267	-0.038593	-0.80952	0.028269	1.7921	-0.39664	0.011426	0.046485	-0.047531	-0.33894	-0.029175	0.0079993	0.028268	0.0013868	0.030851	-0.0029091	-0.036401	-1.2606	-0.017748	-0.86105	-0.42211	-0.027945	-0.045836	0.0015255	0.79937	-0.3311	0.0076392	0.0079175	-0.030267	-0.34916	
Deletion Peak 11 - CN values	14q23.3 	chr14:50572489-104154469(probes 1202060:1235668)  	chr14:65452241-66970919(probes 1211662:1212493)    	chr14:64985729-67242105(probes 1211302:1212554)    	0.14251	    0.14366		Actual Copy Change Given	-0.13797	-0.15511	0.023095	0.00069327	-0.0024258	0.78022	-0.38906	-0.0019399	-0.95403	0.46041	0.056085	-0.70109	-0.18859	-0.019934	0.4536	0.0055314	-0.0078863	0.12653	-1.0627	-0.01037	0.61045	-0.41919	0.0066272	0.035947	-0.0041546	0.0029133	-0.33549	0.41999	0.0066653	0.82529	0.052716	
Deletion Peak 12 - CN values	16q12.1 	chr16:31722415-65161093(probes 1294578:1306703)    	chr16:48114144-48186372(probes 1295277:1295318)    	chr16:31850300-50189592(probes 1294638:1296686)    	0.011674	   0.011453		Actual Copy Change Given	-0.077677	-0.87182	-0.060211	-0.037626	-0.0434	-0.044551	-0.24946	-0.0062381	-0.91736	-0.14493	-0.35658	-0.042302	-0.0048251	-0.3034	-0.24314	-0.027689	0.017124	-0.21911	-1.0648	-0.045906	-0.33179	-0.16841	-0.0041546	-0.0011087	-0.00055444	0.023847	-0.75409	-0.62245	-0.016429	-0.58215	-0.062928	
