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-AF-2691-01A-01D-1167-02	TCGA-AF-2692-01A-01D-1167-02	TCGA-AF-3913-01A-02D-1115-02	TCGA-AG-3574-01A-01D-1167-02	TCGA-AG-3727-01A-01D-1167-02	TCGA-AG-3728-01A-01D-1115-02	TCGA-AG-3878-01A-02D-1167-02	TCGA-AG-3881-01A-01D-0957-02	TCGA-AG-3882-01A-01D-0957-02	TCGA-AG-3885-01A-01D-0957-02	TCGA-AG-3887-01A-01D-1115-02	TCGA-AG-3890-01A-01D-1115-02	TCGA-AG-3892-01A-01D-1115-02	TCGA-AG-3893-01A-01D-1115-02	TCGA-AG-3894-01A-01D-1115-02	TCGA-AG-3896-01A-01D-1115-02	TCGA-AG-3898-01A-01D-1115-02	TCGA-AG-3901-01A-01D-1115-02	TCGA-AG-3902-01A-01D-1115-02	TCGA-AG-3909-01A-01D-1115-02	TCGA-AG-3999-01A-01D-1115-02	TCGA-AG-4001-01A-02D-1115-02	TCGA-AG-4005-01A-01D-1115-02	TCGA-AG-4007-01A-01D-1115-02	TCGA-AG-4008-01A-01D-1115-02	TCGA-AG-4015-01A-01D-1115-02	TCGA-AG-A002-01A-01D-A077-02	TCGA-AG-A008-01A-01D-A077-02	TCGA-AG-A00Y-01A-02D-A077-02	TCGA-AG-A011-01A-01D-A077-02	TCGA-AG-A01N-01A-01D-A077-02	TCGA-AG-A01W-01A-21D-A079-02	TCGA-AG-A01Y-01A-41D-A079-02	TCGA-AG-A020-01A-21D-A079-02	TCGA-AG-A032-01A-01D-A077-02	
Amplification Peak 1	1q42.2 	chr1:232575231-233398748(probes 3051:3071)  	chr1:232575232-233354000(probes 3052:3070)  	chr1:232575232-233623999(probes 3052:3073)  	0.18794	    0.18794		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	1	0	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	2	0	1	
Amplification Peak 2	7p14.1 	chr7:38258354-38623533(probes 17440:17452)    	chr7:38262001-38623532(probes 17445:17451)    	chr7:38259001-38660047(probes 17441:17454)    	0.0063516	  0.0063516		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	2	2	0	0	1	0	0	1	2	1	1	1	2	0	2	2	0	2	1	0	2	0	2	1	2	0	0	0	0	1	1	0	0	0	
Amplification Peak 3	8q24.21	chr8:128117002-129060999(probes 21130:21153)	chr8:128221001-129052000(probes 21133:21152)	chr8:128121001-129162999(probes 21131:21155)	0.070176	   0.070176		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	1	1	1	1	1	0	0	1	0	0	2	0	0	0	0	1	1	0	2	1	2	1	1	2	2	1	0	1	2	2	2	1	2	0	1	
Amplification Peak 4	10q22.3	chr10:75732002-82901999(probes 24065:24184)  	chr10:79726001-82511087(probes 24142:24169)  	chr10:79726001-82924992(probes 24142:24186)  	0.032454	   0.032454		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	2	0	
Amplification Peak 5	12p12.1	chr12:24548909-26825461(probes 27435:27458)  	chr12:24650001-24878640(probes 27436:27445)  	chr12:24650001-25732999(probes 27436:27448)  	0.2155	     0.2155		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	1	0	0	0	2	0	0	1	0	0	0	0	1	0	0	0	0	2	0	0	0	0	0	1	0	0	0	0	0	0	0	1	
Amplification Peak 6	14q11.2	chr14:21724002-22028999(probes 30357:30370)  	chr14:21859001-22000000(probes 30362:30367)  	chr14:21591001-23294736(probes 30338:30391)  	1.0567e-05	 1.0567e-05		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	0	0	2	0	1	0	1	1	0	2	0	1	1	2	0	2	2	1	2	0	1	0	1	0	2	0	0	0	0	1	0	0	
Amplification Peak 7	17q12  	chr17:33976002-35181999(probes 34150:34173)  	chr17:33980001-35164000(probes 34151:34172)  	chr17:33980001-35260505(probes 34151:34175)  	0.2143	     0.2143		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	1	0	0	0	0	2	0	0	0	0	0	0	0	0	1	0	0	
Deletion Peak 1	4q22.1 	chr4:91472002-92233999(probes 10527:10570)	chr4:91971001-92052000(probes 10554:10561)	chr4:91809001-92188000(probes 10544:10567)	0.042212	  0.042212		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	1	1	1	1	1	1	1	0	0	1	0	0	1	1	0	0	
Deletion Peak 2	8p21.2 	chr8:23483002-31455999(probes 19440:19555)	chr8:25049001-25122428(probes 19473:19474)	chr8:25049001-25348777(probes 19473:19477)	0.20496	   0.20496		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	1	1	0	1	1	0	1	0	1	0	1	0	1	0	1	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	1	0	
Deletion Peak 3	16p13.3	chr16:6254001-7422000(probes 32978:33005)  	chr16:6488001-6550000(probes 32988:32989)  	chr16:6254002-7476000(probes 32979:33007)  	0.0087916	 0.0087916		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	2	0	0	1	0	1	0	1	1	0	0	1	0	0	2	0	0	0	0	0	1	0	1	1	0	0	0	0	0	0	0	0	1	
Amplification Peak 1 - CN values	1q42.2 	chr1:232575231-233398748(probes 3051:3071)  	chr1:232575232-233354000(probes 3052:3070)  	chr1:232575232-233623999(probes 3052:3073)  	0.18794	    0.18794		Actual Copy Change Given	0.009529	0.67957	-0.0088526	0	0.87317	0	-0.0046331	0.81318	0.16651	0.010006	0.01396	-0.18991	0.0014872	0.14935	0.050316	-0.051181	0.57594	-0.036946	0.029888	-0.29815	9.4542e-05	-0.24204	0.010146	-0.01904	-0.031768	0.14816	-0.066302	0.24129	0.5182	-0.48823	0.82107	-0.93023	5.7521	-0.024178	0.48129	
Amplification Peak 2 - CN values	7p14.1 	chr7:38258354-38623533(probes 17440:17452)    	chr7:38262001-38623532(probes 17445:17451)    	chr7:38259001-38660047(probes 17441:17454)    	0.0063516	  0.0063516		Actual Copy Change Given	0.02212	0.92959	1.1786	0.0086796	-0.004066	0.51572	-0.84888	0.16085	0.57594	1.4492	0.44992	0.32104	0.59134	3.2036	-0.0033243	1.5468	0.90975	-0.058433	1.1399	0.75657	0	3.8816	0.13057	1.5166	0.39297	3.5577	0.091058	-0.33549	0.27838	0.056678	0.79551	0.40277	0.026416	0.085232	-0.03059	
Amplification Peak 3 - CN values	8q24.21	chr8:128117002-129060999(probes 21130:21153)	chr8:128221001-129052000(probes 21133:21152)	chr8:128121001-129162999(probes 21131:21155)	0.070176	   0.070176		Actual Copy Change Given	0.48613	0.36346	0.69409	0.79954	0.89737	0.084587	0.015888	0.61426	-0.016979	-0.033132	1.0089	0.21763	-0.010922	0.0558	-0.024251	0.61299	0.38254	0.042307	3.4893	0.41814	1.6932	0.83569	0.60666	1.0237	1.1123	0.85205	0.29878	0.77186	1.0727	1.7115	1.7657	0.39944	3.7752	0.087424	0.43456	
Amplification Peak 4 - CN values	10q22.3	chr10:75732002-82901999(probes 24065:24184)  	chr10:79726001-82511087(probes 24142:24169)  	chr10:79726001-82924992(probes 24142:24186)  	0.032454	   0.032454		Actual Copy Change Given	0.010186	-0.1095	-0.051316	-0.019796	-0.0045921	-0.41404	-0.00048099	6	0.052287	-0.072675	-0.86976	-0.10815	-0.17221	-0.12525	-0.12746	-0.094328	-0.15272	-0.029721	-0.059942	-0.28881	0.61529	-0.3224	-0.00307	-0.019314	-0.0066432	-0.5291	-0.17306	0.13515	-0.02149	-0.20125	-0.038586	0.52818	0.00083195	3.1024	-0.10754	
Amplification Peak 5 - CN values	12p12.1	chr12:24548909-26825461(probes 27435:27458)  	chr12:24650001-24878640(probes 27436:27445)  	chr12:24650001-25732999(probes 27436:27448)  	0.2155	     0.2155		Actual Copy Change Given	-0.21076	-0.03038	-0.71749	0.8377	0.018731	-0.38217	-0.01433	1.1738	0.029888	0.0033299	0.61831	0.046418	0.0121	-0.011198	-0.097759	0.51141	-0.33537	0	0	-0.0081624	4.6662	0.28501	-0.014697	-0.020961	0.035524	-1.1103	0.33727	0.16552	0.27496	-0.10952	-0.039073	-0.4627	0.019072	0.038006	0.33232	
Amplification Peak 6 - CN values	14q11.2	chr14:21724002-22028999(probes 30357:30370)  	chr14:21859001-22000000(probes 30362:30367)  	chr14:21591001-23294736(probes 30338:30391)  	1.0567e-05	 1.0567e-05		Actual Copy Change Given	0.01266	0.28929	0.023847	0.0024925	-0.86855	2.0729	-0.41906	0.62715	0.22653	0.86652	0.72609	-0.11952	1.0422	-0.16052	0.57273	0.53696	1.3666	-1.0499	1.5554	1.9212	0.66155	0.98763	0.11829	0.52643	0.05025	0.64763	0.099042	4.4808	-0.061098	0.018555	-0.062934	-0.0013949	0.82138	-0.062738	-0.13644	
Amplification Peak 7 - CN values	17q12  	chr17:33976002-35181999(probes 34150:34173)  	chr17:33980001-35164000(probes 34151:34172)  	chr17:33980001-35260505(probes 34151:34175)  	0.2143	     0.2143		Actual Copy Change Given	-0.0078308	-0.016567	-0.020001	0.089541	0.013729	-0.0043473	-0.055572	0.29199	0.3771	0.042024	0.1179	-0.24776	0.039137	0.18	0.20886	-0.011198	6	-0.00055172	0.75127	0.17257	-0.40189	0.13391	0.048262	1.568	0.14995	0.17875	-0.097778	-0.2708	-0.1583	0.028964	0.24083	0.021973	0.87926	0.013821	0.035895	
Deletion Peak 1 - CN values	4q22.1 	chr4:91472002-92233999(probes 10527:10570)	chr4:91971001-92052000(probes 10554:10561)	chr4:91809001-92188000(probes 10544:10567)	0.042212	  0.042212		Actual Copy Change Given	-0.22219	-0.39797	-0.10092	-0.022321	0	-0.63182	0.009841	-0.42167	-0.016704	-0.05037	0.018821	0.28724	0.021417	0.050345	0.0071168	-0.18055	-0.35119	0.09275	0.10803	-1.086	-0.6154	-1.0169	-0.88268	-0.93429	-0.39608	-0.53134	0.30878	-0.061308	-0.51314	-0.0022332	-0.013532	-0.46217	-0.78942	-0.027769	-0.15187	
Deletion Peak 2 - CN values	8p21.2 	chr8:23483002-31455999(probes 19440:19555)	chr8:25049001-25122428(probes 19473:19474)	chr8:25049001-25348777(probes 19473:19477)	0.20496	   0.20496		Actual Copy Change Given	-0.40955	-0.42735	-0.80675	0.79954	-0.8817	-0.527	0.015888	-0.39486	-0.04726	-1.1002	0.81617	-0.3535	0.013281	-0.6672	0.032422	-0.6836	0.38337	0.030591	-0.5429	-0.67122	-1.0301	-0.98822	-0.58001	-1.0321	-0.64621	-0.51887	-0.4508	-0.5389	-0.80768	-1.0178	-0.90594	-0.20933	-0.7788	-0.34764	0.45847	
Deletion Peak 3 - CN values	16p13.3	chr16:6254001-7422000(probes 32978:33005)  	chr16:6488001-6550000(probes 32988:32989)  	chr16:6254002-7476000(probes 32979:33007)  	0.0087916	 0.0087916		Actual Copy Change Given	-0.01334	-0.02495	-1.4307	0.038107	-0.02334	-0.45601	-0.015553	-0.3982	0.15891	-0.66263	-0.92426	0.1985	0.0019418	-0.71809	0.10072	-0.26752	-1.385	-0.035857	-0.063838	0.29485	0.00051049	0.089272	-0.50381	-0.088772	-0.90169	-0.64349	0.23101	0.94692	0.30904	0.29822	0.69825	0.0070826	0.03369	0	-0.30699	
