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-DX-A2IZ-01A-11D-A21P-01	TCGA-DX-A2J0-01A-11D-A21P-01	TCGA-DX-A2J1-01A-11D-A21P-01	TCGA-DX-A2J4-01A-32D-A21P-01	TCGA-DX-A3LS-01A-11D-A21P-01	TCGA-DX-A3LT-01A-12D-A21P-01	TCGA-DX-A3LU-01A-11D-A21P-01	TCGA-DX-A3LW-01A-21D-A21P-01	TCGA-FX-A3NJ-01A-11D-A21P-01	TCGA-FX-A3NK-01A-11D-A21P-01	TCGA-HB-A2OT-01A-11D-A21P-01	TCGA-HB-A3L4-01A-11D-A21P-01	TCGA-IS-A3K6-01A-11D-A21P-01	TCGA-IS-A3K7-01A-11D-A21P-01	TCGA-IS-A3K8-01A-11D-A21P-01	TCGA-IS-A3KA-01A-11D-A21P-01	TCGA-IW-A3M4-01A-11D-A21P-01	TCGA-IW-A3M5-01A-22D-A21P-01	TCGA-IW-A3M6-01A-11D-A21P-01	TCGA-K1-A3PO-01A-11D-A21P-01	
Amplification Peak  1	1p32.1  	chr1:58400165-60781208(probes 29893:31547)      	chr1:58748371-59471630(probes 30171:30717)      	chr1:58748371-59472396(probes 30171:30720)      	0.21352	    0.21352		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	2	1	0	0	0	1	2	0	0	0	1	0	0	0	0	0	0	0	0	0	
Amplification Peak  2	3q26.31 	chr3:172461349-181441711(probes 354267:358717)	chr3:173975433-174080800(probes 354928:355007)	chr3:173975433-174083757(probes 354928:355010)	0.22271	    0.22271		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	0	0	0	0	0	2	0	0	0	0	1	0	0	0	0	0	0	2	0	0	
Amplification Peak  3	4p15.31 	chr4:11163703-31372566(probes 372474:385937)    	chr4:17904932-18055066(probes 377401:377463)    	chr4:17904932-18058620(probes 377401:377466)    	0.22491	    0.22491		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	0	0	0	0	0	0	1	2	0	0	1	2	0	1	0	2	0	0	0	0	
Amplification Peak  4	5p14.3  	chr5:21898400-21952259(probes 482613:482650)    	chr5:21911015-21926433(probes 482629:482639)    	chr5:21901178-21968731(probes 482614:482652)    	0.060767	    0.17313		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	2	2	0	0	2	0	0	0	0	0	2	0	1	0	0	0	0	0	0	0	
Amplification Peak  5	5p14.2  	chr5:23446521-23595300(probes 483432:483515)    	chr5:23446584-23591454(probes 483433:483514)    	chr5:23435616-23710643(probes 483422:483589)    	0.0050316	    0.14525		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	2	0	0	0	0	2	2	0	0	0	2	0	1	0	0	0	0	0	0	0	
Amplification Peak  6	6p21.1  	chr6:41698135-42692619(probes 595114:595649)    	chr6:42515373-42555783(probes 595559:595571)    	chr6:41700391-42698604(probes 595115:595651)    	0.01032	    0.01032		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	0	0	0	0	0	2	2	0	0	0	1	0	0	0	0	2	0	1	0	0	
Amplification Peak  7	12p13.32	chr12:4550620-5351735(probes 1058044:1058735)    	chr12:5175404-5235861(probes 1058568:1058615)    	chr12:5175404-5238214(probes 1058568:1058618)    	0.24802	    0.24802		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	0	0	2	0	1	0	0	0	0	2	0	0	0	2	0	0	0	1	0	0	
Amplification Peak  8	12q15   	chr12:69178021-69397111(probes 1092662:1092829)	chr12:69183279-69396710(probes 1092663:1092828)	chr12:68940595-71267315(probes 1092542:1094080)	5.2186e-15	 5.2186e-15		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	2	2	2	2	2	2	2	2	0	2	0	0	0	0	0	0	0	0	0	0	
Amplification Peak  9	19p13.3 	chr19:5278879-5450703(probes 1402446:1402522)    	chr19:5279249-5450093(probes 1402447:1402521)    	chr19:5279249-5454762(probes 1402447:1402524)    	0.20837	    0.20837		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	0	1	0	2	0	0	0	1	0	2	0	0	0	0	0	0	0	0	0	0	
Amplification Peak 10	19q13.2 	chr19:39008548-39063136(probes 1417043:1417077)	chr19:39010691-39060025(probes 1417044:1417076)	chr19:39010691-39068640(probes 1417044:1417079)	0.22984	    0.22984		0: t<0.1; 1: 0.1<t< 0.9; 2: t>0.9	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	
Deletion Peak  1	2p23.3 	chr2:1-55246422(probes 129197:161350)               	chr2:24392343-26686725(probes 144470:145492)        	chr2:24406696-24413297(probes 144476:144477)        	0.22099	  0.22099		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0	1	1	0	1	1	
Deletion Peak  2	2q37.3 	chr2:234254888-243199373(probes 255465:260557)  	chr2:242408088-243199373(probes 260512:260557)    	chr2:240533976-243199373(probes 259474:260557)    	0.015163	 0.015163		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	0	0	1	0	0	1	1	1	1	0	1	0	0	1	0	
Deletion Peak  3	3q22.3 	chr3:89150943-178792048(probes 310917:357214)    	chr3:138209982-138488274(probes 336552:336661)    	chr3:138243313-138261776(probes 336568:336569)    	0.22099	  0.22099		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	1	1	0	0	
Deletion Peak  4	4q35.1 	chr4:54241403-191154276(probes 395990:469778)    	chr4:186346211-186465360(probes 468300:468351)    	chr4:186354724-186695207(probes 468302:468541)    	0.22099	  0.22099		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	1	0	0	0	1	1	0	1	0	0	1	1	0	0	0	1	0	1	1	0	
Deletion Peak  5	9p21.3 	chr9:4709005-30412529(probes 832637:848108)        	chr9:21959052-22011391(probes 843307:843348)        	chr9:21320827-22565117(probes 842928:843667)        	0.18353	  0.18353		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	1	0	0	1	0	0	1	0	0	1	0	0	0	1	1	0	
Deletion Peak  6	11q24.3	chr11:56750837-135006516(probes 1009727:1056066)	chr11:128803545-128815336(probes 1052805:1052815)	chr11:128802898-128816305(probes 1052804:1052817)	0.22099	  0.22099		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	1	0	
Deletion Peak  7	12p13.1	chr12:1-31149662(probes 1056067:1074312)           	chr12:12868305-12985542(probes 1062658:1062721)    	chr12:10717443-18958633(probes 1061325:1066331)    	0.18353	  0.18353		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	0	0	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	
Deletion Peak  8	13q14.2	chr13:48666829-51801435(probes 1148547:1149782)  	chr13:49521514-49789163(probes 1149246:1149333)    	chr13:48666829-51631043(probes 1148547:1149671)    	0.015163	 0.015163		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	0	1	1	0	0	1	1	1	1	1	1	0	1	1	0	1	0	
Deletion Peak  9	16p13.3	chr16:1-90354753(probes 1280741:1321556)           	chr16:2070932-2237548(probes 1281109:1281124)        	chr16:2089007-2101748(probes 1281111:1281112)        	0.22428	  0.24542		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	1	0	0	0	0	1	0	0	1	0	0	0	0	1	0	
Deletion Peak 10	19p13.3	chr19:1-59128983(probes 1401246:1425206)           	chr19:686182-1022780(probes 1401316:1401358)          	chr19:713557-753949(probes 1401319:1401320)            	0.22428	  0.24542		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	1	0	1	1	1	
Deletion Peak 11	Xq21.1 	chrX:76710176-77102528(probes 1529113:1529143)    	chrX:76722851-77070309(probes 1529118:1529142)      	chrX:76722851-77001323(probes 1529118:1529138)      	0.22099	  0.22099		0: t>-0.1; 1: -0.1>t> -1.3; 2: t< -1.3	0	1	0	0	0	0	0	1	0	1	1	1	0	1	0	0	1	0	1	0	
Amplification Peak  1 - CN values	1p32.1  	chr1:58400165-60781208(probes 29893:31547)      	chr1:58748371-59471630(probes 30171:30717)      	chr1:58748371-59472396(probes 30171:30720)      	0.21352	    0.21352		Actual Copy Change Given	3.6569	0.10156	0.0021812	0.0063871	0.074804	0.32624	3.6569	0.049824	0.020203	0.0049969	0.34342	-0.047395	0.029494	-0.57694	-0.80495	-0.43572	-0.87276	-0.060341	0.043157	0.00041593	
Amplification Peak  2 - CN values	3q26.31 	chr3:172461349-181441711(probes 354267:358717)	chr3:173975433-174080800(probes 354928:355007)	chr3:173975433-174083757(probes 354928:355010)	0.22271	    0.22271		Actual Copy Change Given	0.022304	-0.0082163	-0.0012473	-0.0027707	0	3.4942	-0.087782	0.0036857	0	-0.64198	0.18837	0.010842	-0.0099288	-0.64725	-0.00086012	0	-0.011473	3.6569	-0.0049844	0.00027728	
Amplification Peak  3 - CN values	4p15.31 	chr4:11163703-31372566(probes 372474:385937)    	chr4:17904932-18055066(probes 377401:377463)    	chr4:17904932-18058620(probes 377401:377466)    	0.22491	    0.22491		Actual Copy Change Given	-0.89037	-0.03073	-0.0023553	-0.0022168	-0.024928	-0.2429	0.53678	3.6569	-0.016841	0.029606	0.31411	0.98846	-0.025866	0.13924	-0.010537	1.569	-0.013127	-0.57245	0.085799	-0.0023553	
Amplification Peak  4 - CN values	5p14.3  	chr5:21898400-21952259(probes 482613:482650)    	chr5:21911015-21926433(probes 482629:482639)    	chr5:21901178-21968731(probes 482614:482652)    	0.060767	    0.17313		Actual Copy Change Given	3.3041	0.91594	-0.0008316	0.003191	3.6569	-0.56366	0.0048942	0.0050532	0.00041593	0.0062481	1.1462	0.040044	0.80873	-0.61945	-0.0014143	-0.042245	0	-0.071812	0.054337	-0.0027707	
Amplification Peak  5 - CN values	5p14.2  	chr5:23446521-23595300(probes 483432:483515)    	chr5:23446584-23591454(probes 483433:483514)    	chr5:23435616-23710643(probes 483422:483589)    	0.0050316	    0.14525		Actual Copy Change Given	3.6569	-0.032094	-0.0008316	0.003191	0.0022262	3.493	3.6569	0.0050532	0.00041593	0.0062481	1.1462	0.040044	0.80873	-0.61945	-0.0014143	-0.042245	0	-0.071812	0.054337	-0.0027707	
Amplification Peak  6 - CN values	6p21.1  	chr6:41698135-42692619(probes 595114:595649)    	chr6:42515373-42555783(probes 595559:595571)    	chr6:41700391-42698604(probes 595115:595651)    	0.01032	    0.01032		Actual Copy Change Given	0.0033509	0.0092554	-0.0013858	0.0012481	0.010571	3.6565	3.6569	0	-0.0085766	0.00041593	0.18413	0.032704	-0.067297	0.086811	-0.0015528	3.6569	-0.03681	0.5162	-0.64424	-0.37977	
Amplification Peak  7 - CN values	12p13.32	chr12:4550620-5351735(probes 1058044:1058735)    	chr12:5175404-5235861(probes 1058568:1058615)    	chr12:5175404-5238214(probes 1058568:1058618)    	0.24802	    0.24802		Actual Copy Change Given	0.0066653	-0.13734	3.6569	-0.00069303	0.6572	-0.80939	-0.0071958	-0.86354	-0.14014	1.886	-0.0013074	-0.010103	-0.54742	1.3263	0.0064976	-0.0501	0.0095883	0.1605	0	-0.0012473	
Amplification Peak  8 - CN values	12q15   	chr12:69178021-69397111(probes 1092662:1092829)	chr12:69183279-69396710(probes 1092663:1092828)	chr12:68940595-71267315(probes 1092542:1094080)	5.2186e-15	 5.2186e-15		Actual Copy Change Given	3.6569	3.6569	3.6569	3.6569	3.6569	3.6569	3.6569	3.6569	-0.14014	3.6569	-0.0013074	0.013416	0.0050248	0.016006	0.0064976	-0.049559	0.0026357	0.0039488	0	-0.0012473	
Amplification Peak  9 - CN values	19p13.3 	chr19:5278879-5450703(probes 1402446:1402522)    	chr19:5279249-5450093(probes 1402447:1402521)    	chr19:5279249-5454762(probes 1402447:1402524)    	0.20837	    0.20837		Actual Copy Change Given	-0.056307	0.16664	-0.0013858	3.6569	-0.033807	-0.26059	-0.023703	0.76792	0.044574	3.1982	-0.054883	-0.051586	0.056684	-0.028765	0.092575	-0.029584	0.035665	-0.61964	-0.14502	0.027919	
Amplification Peak 10 - CN values	19q13.2 	chr19:39008548-39063136(probes 1417043:1417077)	chr19:39010691-39060025(probes 1417044:1417076)	chr19:39010691-39068640(probes 1417044:1417079)	0.22984	    0.22984		Actual Copy Change Given	-0.056307	-0.79831	-0.0013858	3.6569	2.8649	-0.27296	-0.023703	-0.079476	-0.00027724	-0.10788	-0.054883	-0.080008	0.022627	-0.028765	0.092575	-0.12642	-0.83922	0.6953	-0.14502	0.010424	
Deletion Peak  1 - CN values	2p23.3 	chr2:1-55246422(probes 129197:161350)               	chr2:24392343-26686725(probes 144470:145492)        	chr2:24406696-24413297(probes 144476:144477)        	0.22099	  0.22099		Actual Copy Change Given	-0.013127	0.033494	0.0059988	0.0058309	-0.0018072	0.3033	0.0044411	-0.040924	-0.01849	0	-0.19568	-0.95381	0.00433	-0.76715	0.0067758	-0.42571	-0.87767	0.34203	-0.64762	-0.37245	
Deletion Peak  2 - CN values	2q37.3 	chr2:234254888-243199373(probes 255465:260557)  	chr2:242408088-243199373(probes 260512:260557)    	chr2:240533976-243199373(probes 259474:260557)    	0.015163	 0.015163		Actual Copy Change Given	0.00458	0.015672	0.00589	0.0058309	-0.0024869	0.050961	0.0044411	-0.43691	-0.00041585	0.0058309	-0.77841	-0.96853	-0.88246	-0.63708	0.038318	-0.91153	-0.018884	0.055865	-0.64452	0.016006	
Deletion Peak  3 - CN values	3q22.3 	chr3:89150943-178792048(probes 310917:357214)    	chr3:138209982-138488274(probes 336552:336661)    	chr3:138243313-138261776(probes 336568:336569)    	0.22099	  0.22099		Actual Copy Change Given	0.022304	-0.0082163	-0.0012473	-0.0027707	0	-0.53378	-0.087782	0.0036857	0	0.030029	0.18837	0.010842	-0.85304	-0.63034	-0.016778	0	-0.8244	-0.51933	0.047978	0.00027728	
Deletion Peak  4 - CN values	4q35.1 	chr4:54241403-191154276(probes 395990:469778)    	chr4:186346211-186465360(probes 468300:468351)    	chr4:186354724-186695207(probes 468302:468541)    	0.22099	  0.22099		Actual Copy Change Given	-0.90396	-0.046771	-0.0023553	-0.0022168	-0.38055	-0.2429	0.0022193	-0.48395	-0.016841	-0.018353	-0.39867	-0.99708	-0.032606	0.21376	-0.010537	-0.91507	-0.013127	-0.38432	-0.32089	-0.0023553	
Deletion Peak  5 - CN values	9p21.3 	chr9:4709005-30412529(probes 832637:848108)        	chr9:21959052-22011391(probes 843307:843348)        	chr9:21320827-22565117(probes 842928:843667)        	0.18353	  0.18353		Actual Copy Change Given	-0.0053938	0.017769	0.0049969	-0.0026322	-0.37976	-0.018902	0.00597	-0.24302	-0.0038779	0.0048579	-0.22027	0.014051	0.0028024	-0.61863	0.019894	0.27726	0.020497	-1.2929	-1.2929	-0.0031859	
Deletion Peak  6 - CN values	11q24.3	chr11:56750837-135006516(probes 1009727:1056066)	chr11:128803545-128815336(probes 1052805:1052815)	chr11:128802898-128816305(probes 1052804:1052817)	0.22099	  0.22099		Actual Copy Change Given	-0.015054	-1.2676	-0.10092	-0.0016629	-0.00027035	0.70663	-0.0062946	-0.022856	0.0043021	-0.094988	-0.16159	0.019503	0.0065541	-0.056981	0.016676	-0.4695	0.013353	-0.54497	-0.63102	0.0079175	
Deletion Peak  7 - CN values	12p13.1	chr12:1-31149662(probes 1056067:1074312)           	chr12:12868305-12985542(probes 1062658:1062721)    	chr12:10717443-18958633(probes 1061325:1066331)    	0.18353	  0.18353		Actual Copy Change Given	0.0066653	-0.13734	-0.043737	-0.00069303	0.6572	-0.82944	-0.0071958	-0.86354	-0.14014	-0.64067	-0.0013074	-0.95811	-0.54742	0.53731	0.0064976	-0.0501	0.0095883	0.1605	0	-0.0012473	
Deletion Peak  8 - CN values	13q14.2	chr13:48666829-51801435(probes 1148547:1149782)  	chr13:49521514-49789163(probes 1149246:1149333)    	chr13:48666829-51631043(probes 1148547:1149671)    	0.015163	 0.015163		Actual Copy Change Given	0.027919	-0.90003	-0.0018014	-0.0029091	-0.38089	-0.23692	0.0034687	-0.028081	-0.911	-0.51753	-0.18521	-1.2929	-1.2929	-0.64387	-0.018519	-0.47046	-0.88302	0	-0.61575	-0.0055375	
Deletion Peak  9 - CN values	16p13.3	chr16:1-90354753(probes 1280741:1321556)           	chr16:2070932-2237548(probes 1281109:1281124)        	chr16:2089007-2101748(probes 1281111:1281112)        	0.22428	  0.24542		Actual Copy Change Given	-0.025756	0.17303	0.012237	0.0081959	0.0051428	-0.30932	-0.01106	-0.059	0.045424	-0.0078863	-0.34061	-0.0067813	0.032028	-1.2929	0.0362	0.4599	0.054518	-0.087923	-0.601	0.0034687	
Deletion Peak 10 - CN values	19p13.3	chr19:1-59128983(probes 1401246:1425206)           	chr19:686182-1022780(probes 1401316:1401358)          	chr19:713557-753949(probes 1401319:1401320)            	0.22428	  0.24542		Actual Copy Change Given	-0.056307	0.18413	-0.0013858	-0.0037395	-0.033807	-0.26059	-0.023703	-0.77583	0.044574	-0.096044	-0.054883	-0.051586	0.056684	-0.69224	0.092575	-0.43821	0.035665	-0.61964	-0.14502	-0.34423	
Deletion Peak 11 - CN values	Xq21.1 	chrX:76710176-77102528(probes 1529113:1529143)    	chrX:76722851-77070309(probes 1529118:1529142)      	chrX:76722851-77001323(probes 1529118:1529138)      	0.22099	  0.22099		Actual Copy Change Given	-0.063435	-0.1884	0.029606	0.019095	-0.056974	-0.055756	0.038065	-1.2929	-0.082668	-1.0585	-0.17036	-0.47056	0.40681	-0.25479	-0.08243	0.70738	-0.1945	-0.038244	-0.44954	-0.0099288	
