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)  	0.18411	   0.18411		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)    	0.0061204	 0.0061204		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)	0.047114	  0.047114		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	2	1	2	2	1	1	1	2	2	2	1	2	0	1	
Amplification Peak 4	10q22.3 	chr10:75732002-82901999(probes 24119:24238)  	chr10:79726001-82511087(probes 24196:24223)  	chr10:79726001-82924992(probes 24196:24240)  	0.032827	  0.032827		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)  	0.20005	   0.20005		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	1	0	0	0	0	1	0	0	0	0	0	0	0	1	
Amplification Peak 6	13q21.33	chr13:72457001-73489634(probes 29833:29869)  	chr13:72624309-72646000(probes 29843:29844)  	chr13:72624309-72691999(probes 29843:29847)  	0.22454	   0.22454		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	1	2	2	0	2	2	0	0	2	2	2	1	0	2	2	2	0	0	1	1	2	2	2	2	1	2	1	2	2	0	0	0	1	0	2	
Amplification Peak 7	14q11.2 	chr14:21724002-22028999(probes 30424:30437)  	chr14:21859001-22000000(probes 30429:30434)  	chr14:21565001-23294736(probes 30401:30458)  	8.491e-06	 8.491e-06		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 8	17q12   	chr17:33976002-35181999(probes 34225:34248)  	chr17:33980001-35164000(probes 34226:34247)  	chr17:33980001-35260505(probes 34226:34250)  	0.20005	   0.20005		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 	chr4:91315002-92294812(probes 10547:10600)	chr4:91971001-92052000(probes 10578:10585)	chr4:91809001-92180999(probes 10568:10588)	0.13179	   0.13179		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)	0.22262	   0.22262		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)  	0.0087689	 0.0087689		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)  	0.18411	   0.18411		Actual Copy Change Given	0.012802	0.68421	-0.0025642	0.0013357	0.87317	0.0010313	-0.0046331	0.81318	0.16891	0.010006	0.021884	-0.18376	0.0016293	0.15271	0.050853	-0.072541	0.5865	-0.036946	0.031718	-0.30169	0.0023055	-0.19441	0.011818	-0.011335	-0.031359	0.15636	-0.064512	0.25968	0.51836	-0.49352	0.79128	-0.93023	5.7491	-0.024178	0.48335	
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)    	0.0061204	 0.0061204		Actual Copy Change Given	0.025413	0.93467	1.1887	0.010021	-0.004066	0.51701	-0.84888	0.16085	0.5788	1.4492	0.45956	0.32894	0.59152	3.2117	-0.0027707	1.5079	0.92168	-0.058433	1.1427	0.75085	0.0022108	4.0409	0.13234	1.5303	0.39346	3.579	0.092994	-0.32183	0.27852	0.049481	0.76599	0.40277	0.02564	0.085232	-0.028953	
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)	0.047114	  0.047114		Actual Copy Change Given	0.49018	0.36756	0.7026	0.80141	0.89737	0.085684	0.015888	0.61426	-0.014778	-0.033132	1.0207	0.22678	-0.010784	0.059013	-0.023703	0.58435	0.3923	0.042307	3.4943	0.41312	1.6973	0.91253	0.60882	1.0354	1.113	0.86295	0.30185	0.79461	1.0736	1.6985	1.7259	0.39944	3.773	0.087424	0.43659	
Amplification Peak 4 - CN values	10q22.3 	chr10:75732002-82901999(probes 24119:24238)  	chr10:79726001-82511087(probes 24196:24223)  	chr10:79726001-82924992(probes 24196:24240)  	0.032827	  0.032827		Actual Copy Change Given	0.01346	-0.1062	-0.045162	-0.018473	-0.0045921	-0.41322	-0.00048099	6	0.054507	-0.072675	-0.86531	-0.10171	-0.17208	-0.12232	-0.12694	-0.11521	-0.14515	-0.029721	-0.058193	-0.29236	0.61818	-0.27694	-0.0013764	-0.011611	-0.0062286	-0.52348	-0.17137	0.15268	-0.021363	-0.20755	-0.059297	0.52818	6.5258e-05	3.1024	-0.10597	
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)  	0.20005	   0.20005		Actual Copy Change Given	-0.20785	-0.014337	-0.71352	0.83959	0.018731	-0.38134	-0.01433	1.1738	0.03214	0.0033299	0.62861	0.053483	0.012247	-0.0080898	-0.097232	0.48389	-0.32855	0	0.001803	-0.0123	4.6736	0.34693	-0.012697	-0.013264	0.035947	-1.1095	0.33944	0.18329	0.2751	-0.11613	-0.059779	-0.4627	0.018275	0.038006	0.33426	
Amplification Peak 6 - CN values	13q21.33	chr13:72457001-73489634(probes 29833:29869)  	chr13:72624309-72646000(probes 29843:29844)  	chr13:72624309-72691999(probes 29843:29847)  	0.22454	   0.22454		Actual Copy Change Given	0.72412	1.2925	2.3971	-0.034257	1.2253	1.3316	0.0092885	0.044432	1.5084	2.7767	1.0392	0.68496	-0.018902	1.7988	1.1355	2.6628	0.13347	0.031414	0.55744	0.86175	2.1447	1.1819	6	1.1177	0.69764	1.4155	0.49431	1.0433	3.4775	0.0037177	0	0.084354	0.74546	-0.21057	2.006	
Amplification Peak 7 - CN values	14q11.2 	chr14:21724002-22028999(probes 30424:30437)  	chr14:21859001-22000000(probes 30429:30434)  	chr14:21565001-23294736(probes 30401:30458)  	8.491e-06	 8.491e-06		Actual Copy Change Given	0.015937	0.29326	0.030238	0.0038502	-0.86853	2.075	-0.41906	0.62715	0.22901	0.86652	0.73682	-0.11312	1.0424	-0.15764	0.57344	0.50915	1.3804	-1.0499	1.5586	1.9131	0.66449	1.0686	0.12005	0.53626	0.050677	0.65774	0.10099	4.534	-0.060974	0.011514	-0.083388	-0.0013843	0.8203	-0.062738	-0.13489	
Amplification Peak 8 - CN values	17q12   	chr17:33976002-35181999(probes 34225:34248)  	chr17:33980001-35164000(probes 34226:34247)  	chr17:33980001-35260505(probes 34226:34250)  	0.20005	   0.20005		Actual Copy Change Given	-0.0045863	-0.013127	-0.013747	0.090936	0.013729	-0.0033243	-0.055572	0.29199	0.37973	0.042024	0.12623	-0.2418	0.039279	0.18341	0.20947	-0.032996	6	-0.00055172	0.75375	0.16805	-0.40012	0.19173	0.049966	1.5818	0.15039	0.18707	-0.096017	-0.25661	-0.15818	0.021864	0.21717	0.021973	0.87816	0.013821	0.037588	
Deletion Peak 1 - CN values	4q22.1 	chr4:91315002-92294812(probes 10547:10600)	chr4:91971001-92052000(probes 10578:10585)	chr4:91809001-92180999(probes 10568:10588)	0.13179	   0.13179		Actual Copy Change Given	-0.2193	-0.39519	-0.094923	-0.021	0	-0.63112	0.009841	-0.42167	-0.014503	-0.05037	0.026764	0.29502	0.021557	0.053549	0.0076733	-0.2005	-0.34444	0.09275	0.10993	-1.0879	-0.61387	-0.99027	-0.88175	-0.93014	-0.39575	-0.52573	0.31092	-0.045399	-0.51305	-0.0092233	-0.034507	-0.46217	-0.78988	-0.027769	-0.15034	
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)	0.22262	   0.22262		Actual Copy Change Given	-0.40696	-0.42462	-0.80298	0.80141	-0.8817	-0.52624	0.015888	-0.39486	-0.045093	-1.1002	0.82725	-0.3479	0.01342	-0.66511	0.032986	-0.69803	0.39313	0.030591	-0.54159	-0.67398	-1.0291	-0.9608	-0.57882	-1.0283	-0.64593	-0.51321	-0.44937	-0.52691	-0.8076	-1.0212	-0.91749	-0.20933	-0.77927	-0.34764	0.46052	
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)  	0.0087689	 0.0087689		Actual Copy Change Given	-0.010104	-0.021524	-1.4289	0.039468	-0.02334	-0.45522	-0.015553	-0.3982	0.1613	-0.66263	-0.92002	0.20598	0.0020805	-0.71608	0.1013	-0.28651	-1.3825	-0.035857	-0.062092	0.29008	0.0027219	0.14588	-0.50257	-0.081339	-0.90147	-0.63831	0.23307	0.97111	0.30919	0.29018	0.66976	0.0070826	0.032911	0	-0.30558	
