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-C5-A1BQ-01C-11D-A20X-26	TCGA-C5-A2LS-01A-22D-A232-26	TCGA-C5-A2LX-01A-11D-A18I-02	TCGA-C5-A2LZ-01A-11D-A20X-26	TCGA-C5-A2M1-01A-11D-A18I-02	TCGA-C5-A3HD-01B-11D-A20X-26	TCGA-C5-A3HE-01A-21D-A232-26	TCGA-C5-A3HF-01A-11D-A20X-26	TCGA-C5-A3HL-01A-11D-A20X-26	TCGA-EA-A1QS-01A-61D-A232-26	TCGA-EA-A3HQ-01A-11D-A20X-26	TCGA-EA-A3HR-01A-11D-A20X-26	TCGA-EA-A3HS-01A-11D-A20X-26	TCGA-EA-A3HT-01A-61D-A245-26	TCGA-EA-A3HU-01A-11D-A20X-26	TCGA-EA-A3QD-01A-32D-A232-26	TCGA-EA-A3QE-01A-21D-A245-26	TCGA-EA-A3Y4-01A-51D-A245-26	TCGA-EK-A2PL-01A-11D-A18I-02	TCGA-EK-A2PM-01A-11D-A18I-02	TCGA-EK-A2R7-01A-11D-A18I-02	TCGA-EK-A2R8-01A-21D-A18I-02	TCGA-EK-A2RD-01A-12D-A20X-26	TCGA-EK-A2RN-01A-12D-A20X-26	TCGA-EK-A3GJ-01A-21D-A20X-26	TCGA-EK-A3GM-01A-11D-A20X-26	TCGA-EK-A3GN-01A-11D-A20X-26	TCGA-EX-A1H6-01B-11D-A232-26	TCGA-EX-A3L1-01A-11D-A245-26	TCGA-FU-A3EO-01A-11D-A20X-26	TCGA-FU-A3HY-01A-11D-A245-26	TCGA-FU-A3HZ-01A-11D-A20X-26	TCGA-FU-A3NI-01A-11D-A245-26	TCGA-FU-A3TQ-01A-11D-A232-26	TCGA-FU-A3TX-01A-11D-A232-26	TCGA-FU-A3WB-01A-11D-A232-26	TCGA-FU-A3YQ-01A-11D-A232-26	TCGA-HG-A2PA-01A-11D-A20X-26	TCGA-HM-A3JK-01A-11D-A245-26	TCGA-IR-A3L7-01A-21D-A20X-26	TCGA-IR-A3LA-01A-11D-A232-26	TCGA-IR-A3LC-01A-11D-A20X-26	TCGA-IR-A3LF-01A-21D-A232-26	TCGA-IR-A3LH-01A-21D-A20X-26	TCGA-IR-A3LI-01A-11D-A20X-26	TCGA-IR-A3LK-01A-12D-A20X-26	TCGA-IR-A3LL-01A-11D-A20X-26	TCGA-JX-A3PZ-01A-11D-A245-26	TCGA-JX-A3Q0-01A-11D-A245-26	TCGA-JX-A3Q8-01A-11D-A245-26	
Amplification Peak 1	8q24.21 	chr8:128639628-128894353(probes 1709:1746)  	chr8:128747976-128759871(probes 1720:1725)  	chr8:128725907-129070003(probes 1714:1752)	0.0079597	    0.11538		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	1	0	0	2	2	2	1	2	0	0	2	0	0	0	0	2	0	2	0	1	0	0	0	1	1	0	1	0	0	0	0	0	2	0	0	0	1	0	0	0	1	0	0	0	0	1	1	0	0	1	
Amplification Peak 2	8q24.21 	chr8:128860926-129059003(probes 1741:1750)  	chr8:128865436-128892909(probes 1742:1745)  	chr8:128725907-129070003(probes 1714:1752)	0.0040232	   0.044734		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	1	0	0	2	2	2	2	0	0	0	2	0	0	0	0	0	0	2	0	1	0	0	0	1	1	0	1	0	0	0	0	0	2	0	0	0	1	0	0	0	1	0	0	0	0	1	1	0	0	1	
Amplification Peak 3	11q22.1 	chr11:101299139-102362044(probes 2214:2227)	chr11:101443823-102334781(probes 2215:2226)	chr11:99999027-103987372(probes 2205:2237)	0.00050687	 0.00050687		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	0	0	
Amplification Peak 4	19q13.31	chr19:43208675-45519241(probes 3400:3424)    	chr19:44488753-45016256(probes 3404:3415)    	chr19:44488753-45611870(probes 3404:3426)  	0.058226	   0.058226		0: t<0.3; 1: 0.3<t< 0.9; 2: t>0.9	0	0	0	0	1	1	0	0	0	0	0	2	0	0	1	0	1	1	2	0	2	0	0	2	0	2	0	0	0	0	0	0	2	0	0	0	0	0	1	1	0	0	0	1	0	1	1	0	1	0	
Deletion Peak 1	1p36.23 	chr1:1-31732721(probes 1:42)                     	chr1:1-15395210(probes 1:17)                     	chr1:1-15890850(probes 1:20)                     	0.23409	   0.23409		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	1	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	
Deletion Peak 2	2q22.1  	chr2:141742653-141854673(probes 382:387)    	chr2:141796663-141818382(probes 385:386)    	chr2:141591764-142028551(probes 373:405)    	0.0012842	  0.002379		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	1	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	1	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	
Deletion Peak 3	2q36.2  	chr2:202020655-243199373(probes 486:560)    	chr2:221921052-230105901(probes 519:534)    	chr2:202020654-243199373(probes 485:560)    	0.0012842	 0.0012842		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	
Deletion Peak 4	4q35.2  	chr4:174935592-191154276(probes 1017:1038)  	chr4:186870165-191154276(probes 1028:1038)  	chr4:177590600-191154276(probes 1018:1038)  	0.012584	  0.012584		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	0	1	1	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	
Deletion Peak 5	6p12.1  	chr6:41754827-62388977(probes 1228:1285)      	chr6:54412401-57174999(probes 1273:1282)      	chr6:54412401-62388977(probes 1273:1285)      	0.097895	  0.097895		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	
Deletion Peak 6	11q24.1 	chr11:103987375-135006516(probes 2240:2266)	chr11:122397123-135006516(probes 2251:2266)	chr11:103086190-135006516(probes 2236:2266)	0.0012842	 0.0012842		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	1	0	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	1	0	0	1	0	1	0	0	0	1	0	0	0	1	1	0	1	0	0	0	0	1	1	0	1	1	0	1	1	0	0	
Deletion Peak 7	13q13.2 	chr13:28869370-59699592(probes 2459:2516)    	chr13:35242408-37512586(probes 2476:2479)    	chr13:1-60945068(probes 2442:2520)           	0.0012842	 0.0012842		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0	1	1	1	0	1	0	0	0	0	0	0	0	1	1	1	0	0	1	0	1	0	0	0	1	0	0	0	1	0	1	
Deletion Peak 8	14q32.32	chr14:75600050-107349540(probes 2756:2796)  	chr14:102082004-107349540(probes 2783:2796)	chr14:98513920-107349540(probes 2779:2796)  	0.043188	  0.043188		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	
Deletion Peak 9	19p13.3 	chr19:1-9508245(probes 3248:3284)                	chr19:1-1209958(probes 3248:3259)                	chr19:1-1851661(probes 3248:3262)                	0.073418	  0.073418		0: t>-0.3; 1: -0.3>t> -1.3; 2: t< -1.3	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	
Amplification Peak 1 - CN values	8q24.21 	chr8:128639628-128894353(probes 1709:1746)  	chr8:128747976-128759871(probes 1720:1725)  	chr8:128725907-129070003(probes 1714:1752)	0.0079597	    0.11538		Actual Copy Change Given	0.49647	-0.0082083	0.025263	1.0126	6	0.93993	0.49516	2.3856	-0.0039366	0.022858	3.0632	0	0	-0.0085696	-0.0025474	2.0166	0.0022417	1.153	0.049464	0.78069	-0.0047054	0.0064849	0	0.48417	0.40775	-0.56556	0.63548	-1.8838e-05	-0.30941	-0.0088599	0.0039502	-0.0083987	1.5246	0.0049244	-0.50016	0.0051409	0.33988	-0.011745	-0.0022415	0.020124	0.81931	0.010059	-0.0047789	-0.016879	0.024509	0.83522	0.6666	0.0081665	-0.0048791	0.59525	
Amplification Peak 2 - CN values	8q24.21 	chr8:128860926-129059003(probes 1741:1750)  	chr8:128865436-128892909(probes 1742:1745)  	chr8:128725907-129070003(probes 1714:1752)	0.0040232	   0.044734		Actual Copy Change Given	0.49647	-0.0082083	0.025263	1.0126	6	0.93993	6	0.0070062	-0.0039366	0.022858	3.0632	0	0	-0.0085696	-0.0025474	0.038201	0.0022417	1.153	0.049464	0.78069	-0.0047054	0.0064849	0	0.48417	0.40775	-0.56556	0.63548	-1.8838e-05	-0.30941	-0.0088599	0.0039502	-0.0083987	1.5246	0.0049244	-0.50016	0.0051409	0.33988	-0.011745	-0.0022415	0.020124	0.81931	0.010059	-0.0047789	-0.016879	0.024509	0.83522	0.6666	0.0081665	-0.0048791	0.59525	
Amplification Peak 3 - CN values	11q22.1 	chr11:101299139-102362044(probes 2214:2227)	chr11:101443823-102334781(probes 2215:2226)	chr11:99999027-103987372(probes 2205:2237)	0.00050687	 0.00050687		Actual Copy Change Given	-0.065921	-0.008476	-0.70487	-0.21078	0.0051147	0	-0.11771	0.010264	-0.0012979	-0.01009	-0.012435	-0.7526	-0.011028	-0.0049702	-0.0053551	0.97138	0.47503	-0.003626	0.039136	-0.61891	-0.0058329	0	-0.62809	0.0030966	0.99205	-0.022501	-0.0051477	-0.018676	6	0.00024756	0.0040441	-0.0067586	-0.49193	-0.67341	-0.075708	-0.88863	-0.0043652	-0.015516	-0.026398	-0.01121	-0.34105	-0.63079	-0.057483	5.2091	-0.91351	-0.0095737	-0.010489	6	-0.01908	0	
Amplification Peak 4 - CN values	19q13.31	chr19:43208675-45519241(probes 3400:3424)    	chr19:44488753-45016256(probes 3404:3415)    	chr19:44488753-45611870(probes 3404:3426)  	0.058226	   0.058226		Actual Copy Change Given	-0.017182	0.0029277	0.06245	-0.034274	0.70003	0.74001	0.049145	-0.0074731	-0.021449	0.13218	-0.042455	3.2854	-0.048735	-0.008349	0.46236	-0.07577	0.39538	0.54158	1.5275	0.29745	2.6646	0.046293	0.2911	1.2022	-0.39749	1.0911	-0.017124	-0.011474	0.017144	-0.030303	-0.033464	-0.01845	6	-0.046244	0.046424	-0.013591	-0.016223	0	0.30231	0.78318	0.042488	-0.33738	-0.020346	0.66689	-0.02915	0.82423	0.47827	0	0.51079	-0.61459	
Deletion Peak 1 - CN values	1p36.23 	chr1:1-31732721(probes 1:42)                     	chr1:1-15395210(probes 1:17)                     	chr1:1-15890850(probes 1:20)                     	0.23409	   0.23409		Actual Copy Change Given	0.078563	0.00059058	-0.42027	0.31055	0.026349	-0.46799	0.093968	0.067376	0.021313	0.20535	0.74288	-0.73592	0.021104	0.58339	0.022225	0.075056	0.060321	0.01075	0.039786	-0.47394	0.70859	0.053652	0.037459	0.50907	0.037406	-0.54688	0.68804	0.011583	-0.13621	-0.81581	0.01716	0.0018754	-0.014027	0.67678	0.50206	0.0093856	0.016993	0.015088	0.35781	0.03376	0.070048	0.76726	-0.39016	0.02024	0.0063442	0.08327	0.52074	0.041671	0.78698	-0.26088	
Deletion Peak 2 - CN values	2q22.1  	chr2:141742653-141854673(probes 382:387)    	chr2:141796663-141818382(probes 385:386)    	chr2:141591764-142028551(probes 373:405)    	0.0012842	  0.002379		Actual Copy Change Given	-0.70453	0	-0.055417	0.004064	0.014507	-0.076816	-0.21487	-0.0021451	0.00054232	-0.12242	0	-1.4884	0.012989	0.0018696	-0.55114	0.012764	-0.43099	0.0040012	-0.00081406	0.26012	0.0085788	-0.27273	-0.6496	-0.47013	0.0034466	-0.034339	0.019166	0.0059378	-0.049009	0	0.021145	0.0053787	0.48359	0.005607	-0.012628	-0.031321	0.0052305	-0.53065	0.00071633	-1.28	0.0052258	-0.039975	0.006014	-0.0060605	0.017078	-0.022783	0	0.048803	-0.80409	-0.13468	
Deletion Peak 3 - CN values	2q36.2  	chr2:202020655-243199373(probes 486:560)    	chr2:221921052-230105901(probes 519:534)    	chr2:202020654-243199373(probes 485:560)    	0.0012842	 0.0012842		Actual Copy Change Given	-0.069635	0	-0.055417	-0.72099	0.014507	-0.905	-0.21487	-0.0021451	0.00054232	-0.12242	-0.0096039	-0.73812	0.012989	0.0018696	0.031749	-0.53968	-0.44613	0.0040012	-0.00081406	-0.1174	0.0085788	-0.27273	-0.63575	-0.47013	-0.054341	1.1106	0.019166	-0.61674	-0.049009	0	-0.74384	0.0053787	-0.49212	0.005607	-0.012628	-0.88237	0.0052305	0.0084004	-0.067559	-0.031782	0.0052258	-0.039975	0.006014	-0.014012	-0.0061092	-0.81107	-0.51159	-0.81671	-0.0064538	-0.13468	
Deletion Peak 4 - CN values	4q35.2  	chr4:174935592-191154276(probes 1017:1038)  	chr4:186870165-191154276(probes 1028:1038)  	chr4:177590600-191154276(probes 1018:1038)  	0.012584	  0.012584		Actual Copy Change Given	-0.0032154	-0.0052513	-0.51285	0.058723	-0.032663	-0.92479	-0.20011	-0.0086151	0	-0.14381	0.093146	-0.027983	-0.10905	-0.5737	0.0083305	-0.57826	0.45321	-0.0038711	-0.004593	-1.1175	-0.68035	-0.27509	-0.023539	-0.50745	-0.013719	-0.49753	-0.071761	0	-0.34069	-0.011395	0.0038611	-0.0082223	-0.485	0.013798	-0.00019618	0.00729	0.0075507	-0.01578	0	0.013446	-0.89924	0.0052696	0.1118	-0.039078	0	-0.041197	-0.019972	-0.8626	-0.0079785	0.57673	
Deletion Peak 5 - CN values	6p12.1  	chr6:41754827-62388977(probes 1228:1285)      	chr6:54412401-57174999(probes 1273:1282)      	chr6:54412401-62388977(probes 1273:1285)      	0.097895	  0.097895		Actual Copy Change Given	-0.022638	0.0071951	0.017505	-0.021537	0.00078785	-0.88271	0.59905	0.39739	-0.0013712	0.31929	0.0031144	0.037508	0.017672	0.002264	0.010432	0	-0.42605	0.0037707	-0.7436	0.26885	-0.03711	0.032173	0.030537	-0.47059	-0.40335	0	0.034313	-0.61474	0	0.00062244	-0.76076	0.0044046	0	0.0098895	0.032541	0.0067469	0.0077998	0.93432	0.012682	-0.14768	0	-0.0052099	0.20907	0.45495	-0.0011246	0	-0.012842	-1.2026	0.012373	0.58408	
Deletion Peak 6 - CN values	11q24.1 	chr11:103987375-135006516(probes 2240:2266)	chr11:122397123-135006516(probes 2251:2266)	chr11:103086190-135006516(probes 2236:2266)	0.0012842	 0.0012842		Actual Copy Change Given	-0.065921	-0.008476	-0.95245	-0.21078	0.0051147	-0.92317	-0.11771	0.010264	-0.0012979	-0.01009	-0.012435	-0.7526	-0.011028	-0.0049702	-0.0053551	-0.56728	-0.45042	-0.003626	0.016008	-0.61891	-0.0058329	0	-0.62809	0.0030966	-0.83018	-0.022501	-0.0051477	-0.018676	-0.34871	0.00024756	0.0040441	-0.0067586	-0.64394	-0.67341	-0.075708	-0.88863	-0.0043652	-0.015516	-0.026398	-0.01121	-0.71747	-0.63079	-0.057483	-0.4607	-0.91351	-0.045597	-0.54771	-0.8232	-0.01908	0	
Deletion Peak 7 - CN values	13q13.2 	chr13:28869370-59699592(probes 2459:2516)    	chr13:35242408-37512586(probes 2476:2479)    	chr13:1-60945068(probes 2442:2520)           	0.0012842	 0.0012842		Actual Copy Change Given	-0.026955	0.0069906	-0.92763	0.19996	-0.61317	-0.0014294	-0.25313	0.0065949	-0.0099402	-0.16184	-0.038631	-0.033678	-0.020433	0.31357	-0.042592	-0.48985	-0.44105	0.0003692	-0.73973	0.058754	-0.34416	-0.51354	-0.61293	-0.027248	-0.82318	0.052891	-0.019607	-0.0058986	-0.1202	-0.0097389	-0.017409	-0.00016557	-0.44229	-0.6677	-0.66195	-0.0069874	-0.0022668	-0.49893	-0.0018978	-0.80112	-0.030182	-0.03305	0	-0.48351	-0.0072892	-0.0042023	-0.0047118	-0.40337	-0.026248	-0.59112	
Deletion Peak 8 - CN values	14q32.32	chr14:75600050-107349540(probes 2756:2796)  	chr14:102082004-107349540(probes 2783:2796)	chr14:98513920-107349540(probes 2779:2796)  	0.043188	  0.043188		Actual Copy Change Given	0.0086413	-0.000299	-0.86697	-0.0025252	-0.72286	0.010907	-0.22235	-0.00035931	0.004537	0.15257	-0.79764	-0.088744	-0.0093708	-0.0050167	-0.0047456	0.0066599	0.43164	-0.59612	-0.026324	-0.68717	-0.29793	-0.065446	0.023009	0.0064341	0.032433	-0.56643	0.0056183	0.004613	0.086858	-0.0079789	0.77952	0.0037992	0.030623	0.001252	-0.58458	0	0.00050732	0.0064287	-0.0039651	1.6338	-0.87306	0.016604	-0.035804	-0.45941	0.012859	0.012836	0.010454	-0.83087	-0.00012094	0.57406	
Deletion Peak 9 - CN values	19p13.3 	chr19:1-9508245(probes 3248:3284)                	chr19:1-1209958(probes 3248:3259)                	chr19:1-1851661(probes 3248:3262)                	0.073418	  0.073418		Actual Copy Change Given	-0.017182	0.0029277	0.14927	-0.034274	-0.080056	-0.96035	-0.51382	0.0026775	-0.021449	-0.032993	-0.042455	-0.0030023	-0.048735	-0.008349	0.98027	-0.05592	-0.044114	-0.59762	-0.68825	0.026731	0.0098644	-0.24206	-0.026557	-0.55453	-0.33691	-0.45354	-0.75766	-0.011474	0.017144	-0.030303	-0.033464	-0.01845	0.27271	-0.046244	0.046424	-0.013591	-0.016223	0	0.30231	-0.037198	0.16777	-0.9209	-0.020346	0.15322	-0.055145	0.68483	0.47827	-1.2243	0.51079	-0.035842	
