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-IG-A3I8-01A-11D-A248-26	TCGA-IG-A3QL-01A-11D-A248-26	TCGA-IG-A3Y9-01A-12D-A248-26	TCGA-IG-A3YA-01A-11D-A248-26	TCGA-IG-A3YB-01A-11D-A248-26	TCGA-IG-A3YC-01A-11D-A248-26	TCGA-IG-A4P3-01A-11D-A267-26	TCGA-IG-A4QT-01A-21D-A267-26	TCGA-IG-A50L-01A-11D-A267-26	TCGA-IG-A51D-01A-11D-A267-26	TCGA-IG-A5B8-01A-11D-A28P-26	TCGA-IG-A5S3-01A-11D-A28P-26	TCGA-L5-A43C-01A-11D-A248-26	TCGA-L5-A43E-01A-11D-A248-26	TCGA-L5-A43H-01A-11D-A248-26	TCGA-L5-A43I-01A-11D-A248-26	TCGA-L5-A43J-01A-12D-A248-26	TCGA-L5-A43M-01A-11D-A248-26	TCGA-L5-A4OE-01A-11D-A267-26	TCGA-L5-A4OF-01A-11D-A267-26	TCGA-L5-A4OG-01A-11D-A267-26	TCGA-L5-A4OH-01A-11D-A267-26	TCGA-L5-A4OI-01A-11D-A267-26	TCGA-L5-A4OJ-01A-11D-A267-26	TCGA-L5-A4OM-01A-11D-A267-26	TCGA-L5-A4ON-01A-11D-A267-26	TCGA-L5-A4OP-01A-11D-A267-26	TCGA-L5-A4OS-01A-11D-A28P-26	TCGA-L5-A4OT-01A-11D-A28P-26	TCGA-L7-A56G-01A-21D-A267-26	TCGA-LN-A49K-01A-11D-A248-26	TCGA-LN-A49L-01A-11D-A248-26	TCGA-LN-A49M-01A-21D-A267-26	TCGA-LN-A49N-01A-11D-A248-26	TCGA-LN-A49O-01A-11D-A248-26	TCGA-LN-A49P-01A-11D-A248-26	TCGA-LN-A49R-01A-11D-A248-26	TCGA-LN-A49S-01A-11D-A248-26	TCGA-LN-A49U-01A-31D-A267-26	TCGA-LN-A49V-01A-11D-A248-26	TCGA-LN-A49W-01A-11D-A267-26	TCGA-LN-A49X-01A-31D-A267-26	TCGA-LN-A49Y-01A-11D-A267-26	TCGA-LN-A4A2-01A-31D-A267-26	TCGA-LN-A4A3-01A-11D-A267-26	TCGA-LN-A4A4-01A-11D-A267-26	TCGA-LN-A4A6-01A-11D-A267-26	TCGA-LN-A4A8-01A-32D-A267-26	TCGA-LN-A4MQ-01A-11D-A28P-26	TCGA-LN-A4MR-01A-11D-A28P-26	TCGA-LN-A5U5-01A-21D-A28P-26	
Amplification Peak 1	7p11.2 	chr7:54768280-55828923(probes 3972:4009)    	chr7:55222453-55507063(probes 3985:3994)    	chr7:54124133-55955266(probes 3959:4015)    	0.00026716	 0.00026716		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	1	1	0	0	1	0	0	2	1	0	1	0	1	0	2	1	0	1	1	1	1	0	2	0	2	0	1	1	0	0	0	0	0	1	0	1	0	1	2	1	1	2	1	2	2	1	2	0	2	0	
Amplification Peak 2	7q21.3 	chr7:84055159-109068633(probes 4139:4358)  	chr7:92866750-93468698(probes 4227:4230)    	chr7:91954399-95127584(probes 4217:4253)    	0.12576	    0.12576		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	2	0	0	1	2	0	0	1	2	0	1	0	1	0	1	0	0	1	0	1	2	0	0	2	2	0	1	1	0	0	2	0	0	2	1	2	1	1	0	0	2	2	1	2	2	1	1	0	0	0	
Amplification Peak 3	8q24.21	chr8:126775116-129726430(probes 5320:5381)	chr8:128519864-128544592(probes 5361:5362)	chr8:125788275-129949011(probes 5307:5385)	0.0010803	  0.0010803		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	1	2	1	1	1	1	0	0	2	1	2	0	2	2	0	1	2	0	0	0	0	2	1	2	0	2	0	1	1	2	1	2	1	1	2	2	2	1	2	2	1	1	0	2	1	2	1	0	1	2	0	
Amplification Peak 4	11q13.3	chr11:69380205-70286916(probes 6803:6860)  	chr11:69943576-70074236(probes 6842:6849)  	chr11:67250429-72701366(probes 6714:6978)  	1.4369e-28	 1.4369e-28		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	2	0	2	2	0	2	2	0	0	2	0	2	0	0	2	2	0	1	0	0	0	1	0	0	2	0	0	1	0	2	2	0	2	2	0	0	2	0	0	2	2	1	2	2	2	2	2	2	0	2	0	
Deletion Peak 1	2q22.1  	chr2:141721306-142128446(probes 1121:1158)	chr2:141968407-142025552(probes 1142:1145)  	chr2:141756756-142128446(probes 1124:1158)  	0.0088592	   0.067362		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	1	0	1	1	1	0	1	1	0	0	1	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	
Deletion Peak 2	2q22.2  	chr2:142360424-142702424(probes 1177:1208)	chr2:142468582-142497472(probes 1190:1195)  	chr2:142428201-142709102(probes 1180:1210)  	0.014351	   0.077094		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	1	1	0	0	0	1	0	0	0	0	0	0	0	2	
Deletion Peak 3	6p25.3  	chr6:1-5056186(probes 3200:3228)                	chr6:1-2142043(probes 3200:3211)                  	chr6:1-2255176(probes 3200:3214)                  	0.16719	    0.16719		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	0	0	0	0	1	0	1	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	1	1	0	0	0	0	0	0	1	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	
Deletion Peak 4	7q36.1  	chr7:143818945-159138663(probes 4561:4608)	chr7:152099414-154702066(probes 4593:4593)  	chr7:141252004-159138663(probes 4558:4608)  	0.00073159	 0.00073159		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	1	0	1	1	0	1	1	0	0	0	0	1	0	1	0	1	0	1	1	0	
Deletion Peak 5	9p21.3  	chr9:21959090-22010600(probes 5570:5581)    	chr9:21969918-21982367(probes 5571:5574)      	chr9:21410874-24716671(probes 5533:5629)      	1.7151e-34	 1.7151e-34		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	1	1	2	0	1	0	0	0	1	2	0	0	1	1	2	1	0	0	0	1	0	0	2	1	1	0	1	2	1	1	1	1	2	1	1	1	2	0	1	0	2	1	0	2	1	2	1	1	2	
Deletion Peak 6	10p11.21	chr10:34506934-34848990(probes 6020:6041)  	chr10:34509934-34762862(probes 6022:6034)    	chr10:34509934-34795244(probes 6022:6037)    	0.13635	    0.13635		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	0	0	0	1	0	0	1	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	2	
Deletion Peak 7	11q25   	chr11:74482328-135006516(probes 7005:7297)	chr11:130121242-135006516(probes 7280:7297)	chr11:130121242-135006516(probes 7280:7297)	0.13854	    0.13854		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	1	0	0	1	0	1	0	0	1	1	0	0	0	0	0	0	0	0	1	0	1	0	0	1	1	0	1	1	0	0	1	0	0	1	0	0	0	1	1	0	1	1	1	1	0	
Deletion Peak 8	16q23.1 	chr16:78589811-78992298(probes 8780:8796)  	chr16:78684459-78690737(probes 8787:8788)    	chr16:78566536-79009290(probes 8775:8798)    	0.00073159	 0.00073159		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	1	1	0	1	0	2	0	0	1	1	1	1	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	1	1	0	
Amplification Peak 1 - CN values	7p11.2 	chr7:54768280-55828923(probes 3972:4009)    	chr7:55222453-55507063(probes 3985:3994)    	chr7:54124133-55955266(probes 3959:4015)    	0.00026716	 0.00026716		Actual Copy Change Given	0.025723	0.52857	0.86478	0	-0.4397	0.3142	0.27062	0.0031986	2.1548	0.32356	0.2343	0.3779	0.19309	0.46656	0.18632	2.6487	0.30831	-0.010215	0.61934	0.71829	0.35128	0.89212	0.0046018	6	0.29368	1.3909	0.026787	0.36025	0.69073	0.1494	0.20727	-0.8618	-0.02477	0.18429	0.43005	-0.0071486	0.38037	-0.19646	0.79698	6	0.7671	0.36674	6	0.40204	4.8364	1.7637	0.62564	6	0.04012	1.5502	0	
Amplification Peak 2 - CN values	7q21.3 	chr7:84055159-109068633(probes 4139:4358)  	chr7:92866750-93468698(probes 4227:4230)    	chr7:91954399-95127584(probes 4217:4253)    	0.12576	    0.12576		Actual Copy Change Given	0.025723	1.7538	-0.1877	0	0.36012	2.3215	0.051807	0.0031986	0.31142	1.0088	-0.20184	0.36735	0.20437	0.4946	0.18632	0.56192	-0.13396	-0.010215	0.61934	-0.22792	0.35128	0.91375	0.0046018	0.023624	2.1326	1.104	0.026787	0.36025	0.69073	0.1494	0.20727	0.90737	0.02337	0.016527	1.3955	0.83876	1.147	0.42064	0.75729	0.18875	-0.19981	2.8094	6	0.40204	2.4066	1.3347	0.33069	0.74053	0.04012	-0.37139	0.0099164	
Amplification Peak 3 - CN values	8q24.21	chr8:126775116-129726430(probes 5320:5381)	chr8:128519864-128544592(probes 5361:5362)	chr8:125788275-129949011(probes 5307:5385)	0.0010803	  0.0010803		Actual Copy Change Given	0.60887	1.1325	0.41582	0.45645	0.37104	0.69857	0	-0.0046386	6	0.30935	1.1488	-0.099357	5.0857	1.6495	0.18153	0.8385	2.0094	0.00048539	0.061964	0.19985	-0.020472	3.3695	0.82447	6	0.25738	1.5899	0	0.57835	0.32107	0.99808	0.64597	2.1985	0.71072	0.52054	1.3018	1.2711	1.5072	0.78592	1.461	3.0137	0.43058	0.53043	0.10394	1.1949	0.53604	1.7254	0.79176	0	0.32359	1.1834	0.048829	
Amplification Peak 4 - CN values	11q13.3	chr11:69380205-70286916(probes 6803:6860)  	chr11:69943576-70074236(probes 6842:6849)  	chr11:67250429-72701366(probes 6714:6978)  	1.4369e-28	 1.4369e-28		Actual Copy Change Given	6	-0.011961	4.97	2.4666	-0.05695	2.7774	5.6007	-0.013357	-0.034815	6	-0.017352	6	0	-0.0066728	6	0.98958	0.25798	0.50828	0.016325	0.12546	0.017569	0.67537	-0.0034637	0.0032051	6	-0.013194	-0.70335	0.39828	-0.010561	6	1.4867	-0.27582	5.2477	4.9685	0.00070316	-0.033205	5.5171	0.091772	-0.025345	6	2.35	0.53822	5.8725	6	6	6	4.6391	6	0.074329	6	-0.028645	
Deletion Peak 1 - CN values	2q22.1  	chr2:141721306-142128446(probes 1121:1158)	chr2:141968407-142025552(probes 1142:1145)  	chr2:141756756-142128446(probes 1124:1158)  	0.0088592	   0.067362		Actual Copy Change Given	-1.0546	1.1593	-0.49931	0.027035	-0.45392	-0.54943	-0.53557	0.00084731	-0.55552	-0.34395	0.017376	0.45036	-0.40628	-0.015235	-0.94216	0.42345	0.16073	-0.039193	-0.60653	0.088563	0.062412	0.45192	-0.0012294	0.007261	0.65551	-0.0232	-0.74402	-0.15878	-0.058589	-0.013963	0.080741	-0.27487	0.046734	-0.0008563	-0.027339	0.3919	0.033671	-0.20681	0.066658	-0.20865	0.31929	0	-0.91102	-0.064182	0	0.0039323	0.33099	-0.0051491	-0.2417	0.014704	-1.2446	
Deletion Peak 2 - CN values	2q22.2  	chr2:142360424-142702424(probes 1177:1208)	chr2:142468582-142497472(probes 1190:1195)  	chr2:142428201-142709102(probes 1180:1210)  	0.014351	   0.077094		Actual Copy Change Given	-0.031887	1.1593	-0.18609	0.027035	-0.90508	-0.18841	-0.10897	0.00084731	0.032602	0.019156	0.017376	0.45036	-0.40628	-0.015235	-0.29368	0.42345	-0.26838	-0.039193	-0.60653	0.088563	0.062412	0.45192	-0.0012294	0.007261	0.67301	-0.0232	0.021024	-0.15878	-0.058589	-0.55211	0.080741	-0.27487	0.046734	0.023469	-0.027339	-0.36298	0.033671	-0.52383	-1.176	-0.20865	0.31929	0	-0.91102	0.0028667	0	0.0039323	0.33099	-0.0051491	-0.2417	0.014704	-1.3193	
Deletion Peak 3 - CN values	6p25.3  	chr6:1-5056186(probes 3200:3228)                	chr6:1-2142043(probes 3200:3211)                  	chr6:1-2255176(probes 3200:3214)                  	0.16719	    0.16719		Actual Copy Change Given	-0.3696	-0.071391	0.0042873	0.004086	0.051768	0.012312	-0.50987	0.0049095	-0.32364	0.0072393	0.020987	-0.18976	-0.2197	-0.35178	-0.2896	0.43532	-0.60001	0.053316	0.020823	0	-0.3337	0	0.016327	0.020586	0.30652	-0.74517	-0.69622	0.3856	0.026995	-0.0001097	-0.28773	1.3487	0.028173	-0.8585	-0.013553	-0.48333	0.095204	0.045767	0	-0.59322	-0.2453	0.13091	1.0091	-0.44467	0.01354	-0.0033762	-0.014812	-0.00017147	0.29062	0.016015	0.0030062	
Deletion Peak 4 - CN values	7q36.1  	chr7:143818945-159138663(probes 4561:4608)	chr7:152099414-154702066(probes 4593:4593)  	chr7:141252004-159138663(probes 4558:4608)  	0.00073159	 0.00073159		Actual Copy Change Given	0.025723	1.525	-0.30535	0	0.19098	-0.20528	-0.17225	0.0031986	-0.01263	-0.33097	-0.21361	0.36735	-0.22047	0.45513	0.18632	-1.0075	0.25823	-0.010215	0.61058	-0.20193	-0.00021039	0.84893	0.0046018	0.023624	-0.6637	-0.77094	-0.68584	-0.080641	0.051415	0.13543	-0.071143	-0.88836	-0.024665	-0.48535	-0.51023	0.37306	-0.60407	-0.54032	0.75729	0.71283	-0.19981	-0.14894	-0.93713	0.40204	-0.34597	-0.014552	-0.42431	0.74053	-0.59431	-0.37139	0.0099164	
Deletion Peak 5 - CN values	9p21.3  	chr9:21959090-22010600(probes 5570:5581)    	chr9:21969918-21982367(probes 5571:5574)      	chr9:21410874-24716671(probes 5533:5629)      	1.7151e-34	 1.7151e-34		Actual Copy Change Given	-0.63167	0.041446	-0.74253	-0.62795	-1.3186	-0.22325	-0.34022	-0.0047573	-0.27217	0.19387	-1.0114	-1.4873	-0.21236	-0.0086873	-1.0822	-0.57321	-1.5	-0.51123	-0.0025107	-0.25291	0.00099239	-0.95207	-0.0034879	0.0061295	-1.5	-0.75402	-0.71537	-0.15998	-0.64902	-1.3258	-1.2187	-0.86467	-0.72468	-0.99323	-1.3778	-0.83881	-0.60545	-1.2032	-1.5	2.1838	-0.85967	-0.2752	-1.5	-1.27	-0.10656	-1.3031	-1.0519	-1.4165	-0.56017	-1.1733	-1.3726	
Deletion Peak 6 - CN values	10p11.21	chr10:34506934-34848990(probes 6020:6041)  	chr10:34509934-34762862(probes 6022:6034)    	chr10:34509934-34795244(probes 6022:6037)    	0.13635	    0.13635		Actual Copy Change Given	-0.36146	-0.041111	-0.21472	-0.00085164	0.50099	-0.7081	-0.11504	-0.0074519	-0.32433	-0.0094122	-0.2508	-0.45298	0.56768	0	-0.264	0.40007	-0.59575	0.034095	-0.29638	0.52271	-0.3427	0.2037	-0.0030799	0.0025117	-0.075339	0	0.032506	0.063779	-0.23678	-0.18782	-0.059673	1.7816	-0.013586	-0.0035535	-0.91412	-0.0099941	1.4088	0.089872	-0.26437	-0.59782	-0.79962	-0.012575	0.017036	-0.011152	0.0833	0.64669	0.66489	-0.025937	0.19514	-0.39664	-1.3779	
Deletion Peak 7 - CN values	11q25   	chr11:74482328-135006516(probes 7005:7297)	chr11:130121242-135006516(probes 7280:7297)	chr11:130121242-135006516(probes 7280:7297)	0.13854	    0.13854		Actual Copy Change Given	0.021796	-0.011961	-0.030832	-0.0079305	0.35008	-0.22367	-0.43214	-0.013357	0	-0.333	-0.017352	-0.30149	-0.21805	-0.063186	-0.31515	-0.88341	-0.1259	0.26333	0	-0.054968	0.32942	0.4386	-0.0034637	0.0032051	-0.61294	-0.013194	-0.70335	-0.039908	-0.057872	-0.54574	-0.57082	-0.29312	-0.81808	-0.49614	-0.03234	-0.051479	-0.63602	-0.21304	-0.025345	-0.73579	-0.24711	-0.011578	6	-0.45229	-0.46636	-0.038061	-0.38928	-0.71538	-0.59237	-0.41853	-0.028645	
Deletion Peak 8 - CN values	16q23.1 	chr16:78589811-78992298(probes 8780:8796)  	chr16:78684459-78690737(probes 8787:8788)    	chr16:78566536-79009290(probes 8775:8798)    	0.00073159	 0.00073159		Actual Copy Change Given	0.014713	-0.58712	0.34126	-0.0068819	-0.0042651	-0.2434	0.031195	-0.012415	-0.063147	-0.052199	0.55919	0	-0.6889	-0.0028537	0.07137	-1.0186	0.31639	-0.51667	-0.99352	-1.0821	0.31385	-0.91352	-0.22991	-1.4735	-0.061336	-0.17695	-0.75395	-0.31563	-0.69053	-0.55325	-0.10761	-0.29182	-0.014352	-0.013231	-0.39245	-0.0080176	-0.69207	0.49594	-0.087462	-1.0222	-0.015361	-0.021121	0.00038392	-0.12471	0.17121	-0.030171	0.27484	-0.047443	-0.30339	-0.40891	-0.054735	
