Molecular subtypes	CN_CNMF		METHLYATION_CNMF		RPPA_CNMF		RPPA_CHIERARCHICAL		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL	
	nCNV (%)	nWild-Type	Chi-square test_P	Chi-square test_Q	Chi-square test_P	Chi-square test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q	Fisher's exact test_P	Fisher's exact test_Q
Amp Peak  1(1q21.2)	76 (24%)	246	1.2107e-07	6.4e-05	2.627e-08	1.42e-05	0.83774	1	0.35895	1	0.00050944	0.24	0.0031587	1	0.00010279	0.0502	0.27157	1
Amp Peak  2(2q11.2)	69 (21%)	253	3.4769e-06	0.00178	1.7082e-08	9.26e-06	0.93456	1	0.18772	1	0.011931	1	0.080673	1	0.044971	1	0.42876	1
Amp Peak  3(2q31.2)	67 (21%)	255	8.3764e-10	4.61e-07	9.3737e-09	5.09e-06	0.11687	1	0.35895	1	0.31834	1	0.10983	1	0.36728	1	0.081792	1
Amp Peak  4(2q32.2)	59 (18%)	263	7.9674e-07	0.000411	5.3015e-08	2.84e-05	0.049503	1	0.42742	1	0.16897	1	0.0513	1	0.043294	1	0.12919	1
Amp Peak  5(3q26.33)	242 (75%)	80	1.2931e-09	7.09e-07	3.2643e-05	0.0163	0.43466	1	0.26288	1	0.00082912	0.382	0.00028825	0.137	0.0035568	1	0.40632	1
Amp Peak  6(5p15.33)	147 (46%)	175	9.0497e-11	5.02e-08	0.025648	1	0.43657	1	0.51285	1	0.683	1	0.32024	1	0.66485	1	0.17914	1
Amp Peak  7(5p12)	122 (38%)	200	1.834e-10	1.01e-07	0.018165	1	0.82271	1	0.86006	1	0.89962	1	0.38844	1	0.81946	1	0.67627	1
Amp Peak  8(6p12.1)	64 (20%)	258	1.6452e-05	0.00829	0.0028032	1	0.95169	1	0.67624	1	0.98336	1	0.8023	1	0.74389	1	0.6664	1
Amp Peak  9(6q12)	59 (18%)	263	0.00069468	0.323	0.013845	1	0.8781	1	0.52724	1	1	1	0.82193	1	0.70534	1	0.92866	1
Amp Peak 10(7p11.2)	137 (43%)	185	1.9109e-08	1.03e-05	6.8734e-07	0.000356	0.93477	1	0.74965	1	0.50042	1	0.92323	1	0.40492	1	0.19683	1
Amp Peak 11(7q22.1)	114 (35%)	208	3.1022e-11	1.73e-08	5.4553e-08	2.91e-05	0.61697	1	1	1	0.23451	1	0.33488	1	0.06888	1	0.1006	1
Amp Peak 12(8p11.23)	102 (32%)	220	0.040905	1	0.036856	1	0.67261	1	0.41315	1	0.14966	1	0.018247	1	0.012135	1	0.007529	1
Amp Peak 13(8q11.21)	189 (59%)	133	1.0214e-06	0.000525	0.011129	1	0.90232	1	0.76362	1	0.0011291	0.515	0.00066431	0.31	0.066626	1	0.0023008	1
Amp Peak 14(8q24.21)	232 (72%)	90	5.7619e-08	3.07e-05	0.00010584	0.0515	0.2309	1	0.58032	1	0.00010228	0.05	0.00013544	0.0654	0.044151	1	0.00016946	0.0817
Amp Peak 15(9p23)	76 (24%)	246	0.0024819	1	0.78566	1	1	1	0.64697	1	0.099338	1	0.227	1	0.43822	1	0.72779	1
Amp Peak 16(9p13.3)	90 (28%)	232	0.002226	0.999	0.22203	1	0.58747	1	0.16515	1	0.0070808	1	0.037917	1	0.10668	1	0.057361	1
Amp Peak 17(11p13)	63 (20%)	259	0.01767	1	0.097141	1	0.34289	1	0.033001	1	0.63051	1	0.16315	1	0.68237	1	0.96454	1
Amp Peak 18(11p11.2)	63 (20%)	259	0.13959	1	0.53261	1	0.20303	1	0.33584	1	0.62643	1	0.14809	1	0.67082	1	0.33935	1
Amp Peak 19(11q13.3)	146 (45%)	176	1.0363e-23	5.94e-21	0.00089654	0.412	0.90415	1	0.26321	1	0.36071	1	0.50384	1	0.72287	1	0.81015	1
Amp Peak 20(12p13.33)	109 (34%)	213	5.5206e-11	3.07e-08	1.2841e-05	0.0065	0.083623	1	0.41329	1	0.0091238	1	0.0010119	0.462	0.0024677	1	0.81445	1
Amp Peak 21(12q15)	63 (20%)	259	3.7682e-08	2.03e-05	0.0084226	1	0.4252	1	0.099637	1	0.090004	1	0.045857	1	0.48631	1	0.6664	1
Amp Peak 22(13q22.1)	68 (21%)	254	4.1596e-07	0.000218	8.4301e-05	0.0416	0.0070834	1	0.33465	1	0.23284	1	0.0924	1	0.55115	1	0.40929	1
Amp Peak 23(14q11.2)	88 (27%)	234	7.3693e-06	0.00375	0.023941	1	0.63575	1	0.84475	1	0.053001	1	0.38443	1	0.006156	1	0.12594	1
Amp Peak 24(15q26.3)	71 (22%)	251	0.00010641	0.0517	0.21738	1	0.50387	1	0.93242	1	0.92275	1	0.41588	1	0.43969	1	0.26514	1
Amp Peak 25(17q12)	56 (17%)	266	4.9418e-05	0.0246	0.00011155	0.0541	0.94423	1	0.96068	1	0.016761	1	0.030759	1	0.025271	1	0.39947	1
Amp Peak 26(18p11.31)	103 (32%)	219	4.383e-07	0.000229	0.0030633	1	0.87286	1	0.73506	1	0.23777	1	0.16923	1	0.75945	1	0.72989	1
Amp Peak 27(18q11.2)	71 (22%)	251	0.013134	1	0.033009	1	0.46806	1	0.55189	1	1	1	0.68887	1	0.48977	1	0.45143	1
Amp Peak 28(20q11.22)	145 (45%)	177	0.00022537	0.108	0.022198	1	0.43588	1	0.55918	1	0.012787	1	0.085422	1	0.71463	1	0.096487	1
Amp Peak 29(Xq28)	98 (30%)	224	3.9615e-08	2.13e-05	0.003195	1	0.56144	1	0.5784	1	0.1881	1	0.46318	1	0.33848	1	0.20856	1
Del Peak  1(1p36.13)	68 (21%)	254	1.483e-10	8.22e-08	5.3785e-15	3.05e-12	0.0032151	1	0.83955	1	3.0294e-05	0.0152	0.00071584	0.332	0.013084	1	0.066758	1
Del Peak  2(1p13.2)	81 (25%)	241	2.7716e-10	1.53e-07	8.6221e-10	4.73e-07	0.0030098	1	0.047455	1	0.0054596	1	0.09271	1	0.00018064	0.0869	0.97029	1
Del Peak  3(2q21.2)	40 (12%)	282	0.28887	1	0.027827	1	0.73401	1	0.94723	1	0.015371	1	0.0056384	1	0.0034939	1	0.092962	1
Del Peak  4(2q22.1)	66 (20%)	256	0.090593	1	0.0064758	1	0.85523	1	0.33763	1	0.051329	1	0.029155	1	0.095407	1	0.00018615	0.0894
Del Peak  5(2q36.2)	96 (30%)	226	0.00012206	0.0591	5.6852e-06	0.0029	0.24751	1	0.26892	1	0.00063648	0.298	0.0012545	0.571	0.061395	1	0.010583	1
Del Peak  6(3p24.1)	239 (74%)	83	3.2462e-27	1.87e-24	3.9302e-08	2.11e-05	0.18312	1	0.24662	1	0.070659	1	0.36935	1	0.40388	1	0.098285	1
Del Peak  7(3p14.2)	242 (75%)	80	3.4131e-27	1.96e-24	5.7076e-07	0.000298	0.13669	1	0.60315	1	0.11513	1	0.16112	1	0.89503	1	0.12175	1
Del Peak  8(3p12.2)	228 (71%)	94	3.1142e-25	1.79e-22	4.0436e-09	2.2e-06	0.84279	1	0.78402	1	0.24092	1	0.46324	1	0.54087	1	0.12161	1
Del Peak  9(4p16.3)	137 (43%)	185	1.3778e-14	7.8e-12	1.4972e-05	0.00756	0.015601	1	0.71105	1	0.30679	1	0.16064	1	0.11124	1	0.59375	1
Del Peak 10(4p15.2)	138 (43%)	184	7.3603e-16	4.2e-13	5.9825e-07	0.000311	0.020712	1	0.32598	1	0.040558	1	0.012897	1	0.021407	1	0.68735	1
Del Peak 11(4q22.1)	102 (32%)	220	5.4239e-12	3.04e-09	6.4957e-07	0.000337	0.024394	1	0.76907	1	0.37116	1	0.2052	1	0.29252	1	0.70981	1
Del Peak 12(4q35.2)	131 (41%)	191	3.9958e-08	2.14e-05	2.9651e-05	0.0149	0.0040456	1	0.60179	1	0.2748	1	0.35295	1	0.29566	1	0.29223	1
Del Peak 13(5q11.2)	134 (42%)	188	1.6525e-16	9.45e-14	1.3467e-12	7.57e-10	0.095189	1	0.78558	1	0.040089	1	0.00076743	0.355	0.076048	1	0.3975	1
Del Peak 14(5q35.3)	127 (39%)	195	4.0124e-15	2.28e-12	4.2509e-14	2.4e-11	0.24287	1	0.18726	1	0.014627	1	0.00047704	0.225	0.12954	1	0.66263	1
Del Peak 15(6p25.3)	64 (20%)	258	0.0033784	1	0.00033012	0.156	0.034616	1	0.086203	1	0.0075151	1	0.37979	1	0.0053978	1	0.62529	1
Del Peak 16(7q31.1)	49 (15%)	273	0.0019675	0.887	0.026114	1	0.56319	1	0.62391	1	0.36345	1	0.60935	1	0.16719	1	0.27895	1
Del Peak 17(7q36.1)	80 (25%)	242	0.029186	1	0.33047	1	0.25105	1	0.36726	1	0.9573	1	0.67433	1	0.33917	1	0.023668	1
Del Peak 18(8p23.2)	183 (57%)	139	4.9874e-12	2.8e-09	3.8374e-05	0.0191	0.52376	1	0.23725	1	0.016617	1	0.0035288	1	0.058383	1	0.0035505	1
Del Peak 19(9p23)	151 (47%)	171	6.4533e-13	3.63e-10	5.4222e-09	2.95e-06	0.17358	1	0.84502	1	0.73968	1	0.49317	1	0.65216	1	0.22526	1
Del Peak 20(9p21.3)	189 (59%)	133	3.5223e-10	1.94e-07	2.8251e-09	1.54e-06	0.39858	1	0.64555	1	0.39019	1	0.46183	1	0.95805	1	0.6197	1
Del Peak 21(9q21.11)	61 (19%)	261	2.2402e-07	0.000118	0.00096226	0.441	0.57443	1	0.82064	1	0.88221	1	0.67272	1	0.83141	1	0.0214	1
Del Peak 22(9q34.3)	53 (16%)	269	0.00066702	0.311	0.031639	1	0.37444	1	0.11562	1	0.85073	1	0.40851	1	0.47285	1	0.27802	1
Del Peak 23(10p15.3)	108 (34%)	214	1.8402e-05	0.00926	0.029339	1	0.92905	1	0.21816	1	0.32749	1	0.30691	1	0.62101	1	0.47276	1
Del Peak 24(10p11.21)	101 (31%)	221	8.146e-06	0.00413	0.14501	1	0.6028	1	0.09241	1	0.70229	1	0.97498	1	0.9417	1	0.67026	1
Del Peak 25(10q23.31)	83 (26%)	239	0.0045412	1	0.004161	1	0.86452	1	0.69923	1	0.024871	1	0.012786	1	0.27591	1	0.76073	1
Del Peak 26(11p15.4)	102 (32%)	220	3.9138e-06	0.002	0.00052338	0.246	0.42591	1	0.59782	1	0.0022763	1	0.0070965	1	0.0033538	1	0.19607	1
Del Peak 27(11q23.1)	153 (48%)	169	1.3689e-14	7.76e-12	8.4538e-07	0.000435	0.35756	1	0.45285	1	0.00081497	0.377	0.00023024	0.11	0.20714	1	0.18164	1
Del Peak 28(12q24.33)	38 (12%)	284	0.012659	1	0.064574	1	0.024458	1	0.56983	1	0.85888	1	0.77501	1	0.49156	1	0.10981	1
Del Peak 29(13q12.11)	145 (45%)	177	8.0265e-11	4.46e-08	7.2846e-07	0.000377	0.59391	1	0.47444	1	0.053034	1	0.028941	1	0.693	1	0.31855	1
Del Peak 30(13q14.2)	137 (43%)	185	3.1019e-07	0.000163	5.8809e-07	0.000306	0.66087	1	0.25954	1	5.702e-05	0.0283	6.4644e-05	0.032	0.043051	1	0.56812	1
Del Peak 31(14q11.2)	46 (14%)	276	0.026411	1	0.0061601	1	0.51896	1	0.31666	1	0.46295	1	0.3287	1	0.089734	1	0.048668	1
Del Peak 32(14q32.32)	49 (15%)	273	0.28488	1	1.4205e-07	7.5e-05	0.31708	1	0.50706	1	0.00024216	0.116	9.7977e-05	0.048	0.11519	1	0.12581	1
Del Peak 33(15q15.1)	76 (24%)	246	0.0039211	1	0.50124	1	0.38113	1	0.13656	1	0.023265	1	0.048764	1	0.36662	1	0.25453	1
Del Peak 34(16q12.1)	54 (17%)	268	0.073147	1	1.1258e-07	5.97e-05	0.39898	1	0.076822	1	7.1021e-08	3.78e-05	3.9142e-07	0.000205	0.00036952	0.175	0.005852	1
Del Peak 35(16q23.3)	64 (20%)	258	0.073973	1	0.00083917	0.386	0.13323	1	0.03938	1	0.00060143	0.282	8.8834e-05	0.0437	0.033326	1	0.064074	1
Del Peak 36(17q25.3)	41 (13%)	281	0.047891	1	0.12256	1	0.12775	1	0.87457	1	0.036979	1	0.061224	1	0.0071986	1	0.04027	1
Del Peak 37(18q21.2)	170 (53%)	152	3.2133e-14	1.82e-11	1.6888e-09	9.24e-07	0.49717	1	0.49501	1	0.0026752	1	0.0072982	1	0.013346	1	0.031771	1
Del Peak 38(18q23)	182 (57%)	140	2.4202e-16	1.38e-13	1.3766e-11	7.7e-09	0.13635	1	0.21677	1	0.0021609	0.972	0.0033283	1	0.01512	1	0.035911	1
Del Peak 39(19p13.3)	110 (34%)	212	0.0018641	0.843	0.036842	1	0.85219	1	0.075767	1	0.087593	1	0.76122	1	0.75771	1	0.7736	1
Del Peak 40(19q13.43)	64 (20%)	258	9.256e-05	0.0454	6.9318e-05	0.0342	0.67142	1	0.13842	1	0.58361	1	0.26181	1	0.057815	1	0.77423	1
Del Peak 41(Xp21.3)	106 (33%)	216	7.7323e-06	0.00393	0.0053235	1	0.13907	1	0.037111	1	0.27514	1	0.041471	1	0.12142	1	0.83428	1
Del Peak 42(Xp11.3)	108 (34%)	214	9.6946e-08	5.15e-05	5.7969e-05	0.0288	0.13907	1	0.0049951	1	0.211	1	0.059839	1	0.17594	1	0.20982	1
Del Peak 43(Xq21.33)	55 (17%)	267	1.0691e-06	0.000548	0.0016593	0.752	0.032215	1	0.70126	1	0.0013088	0.594	0.012344	1	0.00032372	0.154	0.0052434	1