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-A51D-01A-11D-A267-26	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-A4OP-01A-11D-A267-26	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-A4A2-01A-31D-A267-26	TCGA-LN-A4A3-01A-11D-A267-26	TCGA-LN-A4A4-01A-11D-A267-26	
Amplification Peak 1	11q13.3	chr11:69467999-70286916(probes 4651:4692)	chr11:69943576-70074236(probes 4676:4683)	chr11:68638568-72117700(probes 4598:4750)	1.5678e-20	 1.5678e-20		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	2	0	2	2	0	2	2	0	0	2	2	0	1	0	0	0	1	0	2	2	0	2	2	0	0	2	0	0	2	2	2	2	
Deletion Peak 1	2q22.2 	chr2:142380819-142702424(probes 765:792)  	chr2:142468582-142497472(probes 774:779)  	chr2:142433201-142709102(probes 766:794)  	0.015854	   0.015854		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	1	0	0	1	0	1	0	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	1	0	0	0	0	
Deletion Peak 2	3p11.1 	chr3:74312399-94258261(probes 1203:1257)    	chr3:86787490-89491401(probes 1232:1245)    	chr3:77733046-94472024(probes 1206:1259)    	0.025299	   0.025299		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	1	0	0	1	0	0	0	0	1	0	1	1	0	0	0	1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	1	
Deletion Peak 3	6p25.3 	chr6:1-28732470(probes 2166:2244)              	chr6:1-2142043(probes 2166:2177)                	chr6:1-2255176(probes 2166:2180)                	0.20887	    0.20887		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	1	0	0	0	0	1	0	1	0	0	0	1	1	0	0	
Deletion Peak 4	7q36.1 	chr7:141204815-159138663(probes 3061:3098)	chr7:147704425-159138663(probes 3069:3098)	chr7:143818946-159138663(probes 3066:3098)	0.041608	   0.041608		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	1	0	1	1	0	1	1	0	0	0	0	0	
Deletion Peak 5	9p21.3 	chr9:21959090-22010600(probes 3766:3775)    	chr9:21969918-22000470(probes 3767:3774)    	chr9:21562561-24573438(probes 3745:3807)    	3.4142e-22	 3.4142e-22		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	1	1	2	0	0	0	0	1	1	2	1	0	0	0	1	1	2	1	1	1	1	2	1	1	1	2	0	1	0	2	
Deletion Peak 6	16q23.1	chr16:78589811-78992298(probes 5974:5990)  	chr16:78684459-78690737(probes 5981:5982)  	chr16:78589810-79085899(probes 5973:5995)  	0.0010212	  0.0010212		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	1	0	0	0	0	0	1	0	0	1	0	1	1	1	0	1	1	1	0	1	0	0	1	0	1	0	0	1	0	0	0	
Amplification Peak 1 - CN values	11q13.3	chr11:69467999-70286916(probes 4651:4692)	chr11:69943576-70074236(probes 4676:4683)	chr11:68638568-72117700(probes 4598:4750)	1.5678e-20	 1.5678e-20		Actual Copy Change Given	6	-0.014005	5.7161	2.4666	-0.048129	2.7778	6	0.0058807	-0.0063923	6	0.9871	0.23205	0.50896	0.016324	0.12759	0.016568	0.65973	-0.70489	6	1.594	-0.33384	5.2418	4.9685	0.0019006	-0.025537	5.5694	0.090817	-0.026882	6	6	6	6	
Deletion Peak 1 - CN values	2q22.2 	chr2:142380819-142702424(probes 765:792)  	chr2:142468582-142497472(probes 774:779)  	chr2:142433201-142709102(probes 766:794)  	0.015854	   0.015854		Actual Copy Change Given	-0.019739	1.1591	-0.19226	0.027246	-0.90508	-0.18827	0.019156	-0.4016	-0.016674	-0.37709	0.41331	-0.28827	-0.038663	-0.60653	0.090662	0.061389	0.43758	0	-0.55211	0.14473	-0.33292	0.045077	0.023469	-0.03087	-0.36533	0.0058976	-0.52383	-1.2063	-0.11381	0.024281	0	0.0028977	
Deletion Peak 2 - CN values	3p11.1 	chr3:74312399-94258261(probes 1203:1257)    	chr3:86787490-89491401(probes 1232:1245)    	chr3:77733046-94472024(probes 1206:1259)    	0.025299	   0.025299		Actual Copy Change Given	-0.76044	-0.50213	-0.18218	-0.21278	-0.91105	-0.23158	-0.031358	-0.011274	-0.13447	-0.52274	-0.14888	-0.63606	-0.5097	-0.079904	0.31401	-0.011288	-0.48565	-0.71738	-0.54153	-0.43174	-0.9315	-0.44694	-0.50541	-0.47325	0.29539	-0.6181	-0.35021	-0.75403	-1.0041	-0.0085964	-0.31745	-0.62122	
Deletion Peak 3 - CN values	6p25.3 	chr6:1-28732470(probes 2166:2244)              	chr6:1-2142043(probes 2166:2177)                	chr6:1-2255176(probes 2166:2180)                	0.20887	    0.20887		Actual Copy Change Given	-0.35954	-0.071391	0.0097163	0.004086	0.051768	0.012476	0.0072393	-0.21446	-0.35178	-0.2896	0.4333	-0.61609	0.053871	0.020823	0	-0.33452	-0.010599	-0.69711	-0.0001097	-0.23507	1.2152	0.026531	-0.8585	-0.012364	-0.48784	0.088976	0.089335	-0.0015564	-0.51874	-0.42804	0.01354	-0.004407	
Deletion Peak 4 - CN values	7q36.1 	chr7:141204815-159138663(probes 3061:3098)	chr7:147704425-159138663(probes 3069:3098)	chr7:143818946-159138663(probes 3066:3098)	0.041608	   0.041608		Actual Copy Change Given	0.038226	1.525	-0.31524	0	0.59004	-0.20513	-0.33097	-0.21523	0.45513	0.18632	-1.0083	0.3268	-0.0082493	0.60704	-0.20012	-0.0012022	0.81652	-0.6874	0.13031	-0.011823	-0.69137	-0.03505	-0.47267	-0.49812	0.36965	-0.59906	-0.54032	0.75515	0.85646	0.42811	-0.12552	-0.015577	
Deletion Peak 5 - CN values	9p21.3 	chr9:21959090-22010600(probes 3766:3775)    	chr9:21969918-22000470(probes 3767:3774)    	chr9:21562561-24573438(probes 3745:3807)    	3.4142e-22	 3.4142e-22		Actual Copy Change Given	-0.59557	0.041446	-0.73912	-0.62795	-1.3186	-0.22311	0.22103	-0.2071	-0.0086873	-1.0822	-0.5744	-1.5	-0.51083	0	-0.25116	0	-0.9582	-0.71689	-1.3258	-1.1947	-0.90288	-0.7337	-0.99323	-1.3774	-0.84048	-0.60045	-1.2032	-1.5	2.4124	-1.2622	-0.10656	-1.3035	
Deletion Peak 6 - CN values	16q23.1	chr16:78589811-78992298(probes 5974:5990)  	chr16:78684459-78690737(probes 5981:5982)  	chr16:78589810-79085899(probes 5973:5995)  	0.0010212	  0.0010212		Actual Copy Change Given	0.027149	-0.58712	0.3476	-0.0068819	-0.0059513	-0.24325	-0.052199	-0.68504	-0.0028537	0.07137	-1.0715	0.28978	-0.51627	-0.99963	-1.0812	0.30866	-0.91987	-0.75543	-0.55325	-0.049411	-0.30701	-0.01596	-0.013231	-0.39151	-0.014791	-0.74702	0.50426	-0.092751	-0.97046	-0.10184	0.17121	-0.031188	
