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 3053:3073)  	chr1:232575232-233354000(probes 3054:3072)  	chr1:232575232-233623999(probes 3054:3075)  	0.18689	    0.18689		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 17477:17489)    	chr7:38262001-38623532(probes 17482:17488)    	chr7:38259001-38660047(probes 17478:17491)    	0.0063117	  0.0063117		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 21174:21197)	chr8:128221001-129052000(probes 21177:21196)	chr8:128121001-129162999(probes 21175:21199)	0.065498	   0.065498		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	chr10:79714741-82901999(probes 24195:24238)  	chr10:79726001-82511087(probes 24196:24223)  	chr10:79726001-82924992(probes 24196:24240)  	0.032248	   0.032248		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 27497:27520)  	chr12:24650001-24878640(probes 27498:27507)  	chr12:24650001-25732999(probes 27498:27510)  	0.20965	    0.20965		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 30424:30437)  	chr14:21859001-22000000(probes 30429:30434)  	chr14:21565001-23294736(probes 30401:30458)  	1.0463e-05	 1.0463e-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 34225:34248)  	chr17:33980001-35164000(probes 34226:34247)  	chr17:33980001-35260505(probes 34226:34250)  	0.20627	    0.20627		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 10551:10594)	chr4:91971001-92052000(probes 10578:10585)	chr4:91809001-92188000(probes 10568:10591)	0.044753	  0.044753		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 19477:19592)	chr8:25049001-25122428(probes 19510:19511)	chr8:25049001-25348777(probes 19510:19514)	0.21539	   0.21539		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 33049:33076)  	chr16:6488001-6550000(probes 33059:33060)  	chr16:6254002-7476000(probes 33050:33078)  	0.0093754	 0.0093754		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 3053:3073)  	chr1:232575232-233354000(probes 3054:3072)  	chr1:232575232-233623999(probes 3054:3075)  	0.18689	    0.18689		Actual Copy Change Given	0.009529	0.67957	-0.0088526	0	0.87317	0	-0.0046331	0.81318	0.16651	0.010006	0.013954	-0.18991	0.0014906	0.14965	0.050285	-0.051181	0.57594	-0.036946	0.029888	-0.29815	9.4542e-05	-0.24204	0.011818	-0.01904	-0.031768	0.14816	-0.066302	0.24127	0.51701	-0.48823	0.82107	-0.93023	5.7521	-0.024178	0.48129	
Amplification Peak 2 - CN values	7p14.1 	chr7:38258354-38623533(probes 17477:17489)    	chr7:38262001-38623532(probes 17482:17488)    	chr7:38259001-38660047(probes 17478:17491)    	0.0063117	  0.0063117		Actual Copy Change Given	0.02212	0.92959	1.1786	0.0086796	-0.004066	0.51571	-0.84888	0.16085	0.57594	1.4492	0.44991	0.32104	0.59134	3.2043	-0.0033243	1.5468	0.90975	-0.058433	1.1399	0.75657	0	3.8816	0.13234	1.5166	0.39297	3.5577	0.091058	-0.33551	0.27729	0.056678	0.79551	0.40277	0.026416	0.085232	-0.03059	
Amplification Peak 3 - CN values	8q24.21	chr8:128117002-129060999(probes 21174:21197)	chr8:128221001-129052000(probes 21177:21196)	chr8:128121001-129162999(probes 21175:21199)	0.065498	   0.065498		Actual Copy Change Given	0.48613	0.36346	0.69409	0.79954	0.89737	0.084609	0.015888	0.61426	-0.016979	-0.033132	1.0089	0.21923	-0.010922	0.056085	-0.024251	0.61299	0.38254	0.042307	3.4893	0.41814	1.6932	0.83569	0.60882	1.0237	1.1123	0.85205	0.29972	0.77184	1.0719	1.7115	1.7657	0.39944	3.7752	0.087424	0.43456	
Amplification Peak 4 - CN values	10q22.3	chr10:79714741-82901999(probes 24195:24238)  	chr10:79726001-82511087(probes 24196:24223)  	chr10:79726001-82924992(probes 24196:24240)  	0.032248	   0.032248		Actual Copy Change Given	0.010186	-0.10948	-0.051316	-0.019796	-0.0045921	-0.41404	-0.00048099	6	0.05223	-0.072675	-0.86976	-0.10815	-0.17221	-0.12499	-0.12746	-0.094328	-0.15272	-0.029721	-0.059942	-0.28881	0.61529	-0.3224	-0.0013764	-0.019314	-0.0066432	-0.5291	-0.17306	0.13514	-0.02243	-0.20125	-0.038586	0.52818	0.00083195	3.1024	-0.10754	
Amplification Peak 5 - CN values	12p12.1	chr12:24548909-26825461(probes 27497:27520)  	chr12:24650001-24878640(probes 27498:27507)  	chr12:24650001-25732999(probes 27498:27510)  	0.20965	    0.20965		Actual Copy Change Given	-0.21076	-0.017775	-0.71757	0.8377	0.018731	-0.38217	-0.01433	1.1738	0.029888	0.0033299	0.6183	0.04652	0.012107	-0.010922	-0.097759	0.51141	-0.33537	0	0	-0.0081624	4.6662	0.28501	-0.012697	-0.020961	0.035524	-1.1129	0.33727	0.1655	0.27388	-0.10952	-0.039073	-0.4627	0.019048	0.038006	0.33232	
Amplification Peak 6 - CN values	14q11.2	chr14:21724002-22028999(probes 30424:30437)  	chr14:21859001-22000000(probes 30429:30434)  	chr14:21565001-23294736(probes 30401:30458)  	1.0463e-05	 1.0463e-05		Actual Copy Change Given	0.01266	0.28929	0.023847	0.0025128	-0.86853	2.0729	-0.41906	0.62715	0.22653	0.86652	0.72609	-0.11952	1.0422	-0.16026	0.57273	0.53696	1.3666	-1.0499	1.5554	1.9212	0.66155	0.98763	0.12005	0.52643	0.05025	0.64763	0.099042	4.4808	-0.06202	0.018577	-0.062934	-0.0013843	0.82138	-0.062738	-0.13644	
Amplification Peak 7 - CN values	17q12  	chr17:33976002-35181999(probes 34225:34248)  	chr17:33980001-35164000(probes 34226:34247)  	chr17:33980001-35260505(probes 34226:34250)  	0.20627	    0.20627		Actual Copy Change Given	-0.0078308	-0.016567	-0.020001	0.089541	0.013729	-0.0043534	-0.055572	0.29199	0.3771	0.042024	0.11789	-0.24776	0.039137	0.1803	0.20886	-0.011198	6	-0.00055172	0.75127	0.17257	-0.40189	0.13391	0.049966	1.568	0.14995	0.17875	-0.097778	-0.27081	-0.15917	0.028964	0.24083	0.021973	0.87926	0.013821	0.035895	
Deletion Peak 1 - CN values	4q22.1 	chr4:91472002-92233999(probes 10551:10594)	chr4:91971001-92052000(probes 10578:10585)	chr4:91809001-92188000(probes 10568:10591)	0.044753	  0.044753		Actual Copy Change Given	-0.22219	-0.39797	-0.10092	-0.022321	0	-0.63182	0.009841	-0.42167	-0.016704	-0.05037	0.018815	0.28724	0.021417	0.050629	0.0071168	-0.18055	-0.35119	0.09275	0.10803	-1.086	-0.6154	-1.0169	-0.88175	-0.93429	-0.39608	-0.53134	0.30878	-0.061324	-0.51385	-0.0022332	-0.013532	-0.46217	-0.78942	-0.027769	-0.15187	
Deletion Peak 2 - CN values	8p21.2 	chr8:23483002-31455999(probes 19477:19592)	chr8:25049001-25122428(probes 19510:19511)	chr8:25049001-25348777(probes 19510:19514)	0.21539	   0.21539		Actual Copy Change Given	-0.40955	-0.42735	-0.80675	0.79954	-0.8817	-0.527	0.015888	-0.39486	-0.04726	-1.1002	0.81616	-0.3535	0.013281	-0.66701	0.032422	-0.6836	0.38337	0.030591	-0.5429	-0.67122	-1.0301	-0.98822	-0.57882	-1.0321	-0.64621	-0.51887	-0.4508	-0.53891	-0.80825	-1.0178	-0.90594	-0.20933	-0.7788	-0.34764	0.45847	
Deletion Peak 3 - CN values	16p13.3	chr16:6254001-7422000(probes 33049:33076)  	chr16:6488001-6550000(probes 33059:33060)  	chr16:6254002-7476000(probes 33050:33078)  	0.0093754	 0.0093754		Actual Copy Change Given	-0.01334	-0.02495	-1.4307	0.038107	-0.02334	-0.45602	-0.015553	-0.3982	0.15891	-0.66263	-0.92426	0.1985	0.0019418	-0.71791	0.10072	-0.26752	-1.385	-0.035857	-0.063838	0.29485	0.00051049	0.089272	-0.50257	-0.088772	-0.90169	-0.64349	0.23101	0.9469	0.30794	0.29822	0.69825	0.0070826	0.03369	0	-0.30699	
