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)	82 (23%)	270	8.5112e-11	4.55e-08	2.627e-08	1.36e-05	0.47319	1	0.71766	1	0.00050944	0.23	0.0031587	1	0.00013618	0.0636	0.53467	1
Amp Peak  2(2q11.2)	74 (21%)	278	2.497e-08	1.29e-05	1.7082e-08	8.87e-06	0.99085	1	0.29511	1	0.011931	1	0.080673	1	0.0031888	1	0.10481	1
Amp Peak  3(2q31.2)	72 (20%)	280	1.2625e-10	6.74e-08	9.3737e-09	4.89e-06	0.80315	1	0.50916	1	0.31834	1	0.10983	1	0.22992	1	0.51905	1
Amp Peak  4(3q26.33)	264 (75%)	88	2.9435e-13	1.6e-10	8.7128e-05	0.0413	0.24361	1	0.19274	1	0.0012816	0.551	0.00046752	0.212	0.0010269	0.447	0.068566	1
Amp Peak  5(5p15.33)	157 (45%)	195	1.3128e-11	7.08e-09	0.025648	1	0.62408	1	0.28223	1	0.683	1	0.32024	1	0.68097	1	0.63795	1
Amp Peak  6(5p12)	131 (37%)	221	3.4758e-12	1.88e-09	0.018165	1	0.47808	1	1	1	0.89962	1	0.38844	1	0.84119	1	0.90487	1
Amp Peak  7(6p12.1)	70 (20%)	282	0.00019536	0.0908	0.0028032	1	0.3028	1	0.46985	1	0.98336	1	0.8023	1	0.92805	1	0.0166	1
Amp Peak  8(6q12)	62 (18%)	290	0.00040012	0.182	0.013845	1	0.81119	1	0.3733	1	1	1	0.82193	1	0.69689	1	0.068181	1
Amp Peak  9(7p11.2)	147 (42%)	205	1.1216e-08	5.84e-06	6.8734e-07	0.000346	0.25991	1	0.83177	1	0.50042	1	0.92323	1	0.864	1	0.087623	1
Amp Peak 10(7q22.1)	121 (34%)	231	6.9866e-15	3.81e-12	5.4553e-08	2.8e-05	0.5988	1	0.56748	1	0.23451	1	0.33488	1	0.01811	1	0.57756	1
Amp Peak 11(8p11.23)	111 (32%)	241	0.035189	1	0.036856	1	0.89679	1	0.62925	1	0.14966	1	0.018247	1	0.020315	1	0.14956	1
Amp Peak 12(8q11.21)	207 (59%)	145	1.7966e-06	0.000895	0.011129	1	0.03226	1	0.51802	1	0.0011291	0.49	0.00066431	0.296	0.002403	1	0.0040338	1
Amp Peak 13(8q24.21)	254 (72%)	98	3.3119e-10	1.76e-07	0.00010584	0.0497	0.18972	1	0.91692	1	0.00010228	0.0482	0.00013544	0.0634	0.012799	1	0.0011423	0.495
Amp Peak 14(9p23)	83 (24%)	269	3.1858e-05	0.0155	0.78566	1	0.65522	1	0.88824	1	0.099338	1	0.227	1	0.36467	1	0.93661	1
Amp Peak 15(9p13.3)	95 (27%)	257	5.0563e-05	0.0244	0.22203	1	0.38958	1	0.25442	1	0.0070808	1	0.037917	1	0.0059889	1	0.068386	1
Amp Peak 16(11p13)	69 (20%)	283	5.6581e-05	0.0272	0.097141	1	0.18692	1	0.053918	1	0.63051	1	0.16315	1	0.40251	1	0.024643	1
Amp Peak 17(11q13.3)	164 (47%)	188	1.7288e-27	9.63e-25	0.00089654	0.394	0.90147	1	0.28425	1	0.36071	1	0.50384	1	0.62675	1	0.11041	1
Amp Peak 18(12p13.33)	118 (34%)	234	2.8492e-10	1.52e-07	1.2841e-05	0.00628	0.27581	1	0.35153	1	0.0091238	1	0.0010119	0.441	0.0017731	0.754	0.6961	1
Amp Peak 19(12q15)	72 (20%)	280	0.00050814	0.23	0.0084226	1	0.060942	1	0.19277	1	0.090004	1	0.045857	1	0.49783	1	0.83816	1
Amp Peak 20(13q22.1)	72 (20%)	280	0.00026247	0.121	8.4301e-05	0.0401	0.018087	1	0.20522	1	0.23284	1	0.0924	1	0.09537	1	0.13473	1
Amp Peak 21(15q26.3)	75 (21%)	277	0.000327	0.151	0.21738	1	0.26329	1	0.62361	1	0.92275	1	0.41588	1	0.91822	1	0.45668	1
Amp Peak 22(17q12)	63 (18%)	289	8.1992e-08	4.2e-05	0.00011155	0.0523	0.62283	1	0.72953	1	0.016761	1	0.030759	1	0.031294	1	0.61526	1
Amp Peak 23(18p11.31)	108 (31%)	244	7.5847e-07	0.00038	0.0031528	1	0.96239	1	0.76598	1	0.26152	1	0.20601	1	0.57771	1	0.97402	1
Amp Peak 24(18q11.2)	74 (21%)	278	0.017365	1	0.033009	1	0.15741	1	0.46194	1	1	1	0.68887	1	0.16945	1	0.34275	1
Amp Peak 25(20q11.22)	155 (44%)	197	4.8579e-06	0.0024	0.022198	1	0.84515	1	0.44182	1	0.012787	1	0.085422	1	0.2564	1	0.016892	1
Del Peak  1(1p36.13)	69 (20%)	283	1.4356e-11	7.71e-09	5.3785e-15	2.94e-12	0.022519	1	0.73943	1	3.0294e-05	0.0148	0.00071584	0.318	0.00034954	0.16	0.14105	1
Del Peak  2(1p13.2)	85 (24%)	267	3.101e-10	1.65e-07	8.6221e-10	4.56e-07	0.012405	1	0.11798	1	0.0054596	1	0.09271	1	8.457e-05	0.0402	0.82787	1
Del Peak  3(1q44)	30 (9%)	322	0.13915	1	0.17517	1	0.85891	1	0.93136	1	0.062774	1	0.013281	1	0.0047114	1	0.24475	1
Del Peak  4(2q21.2)	46 (13%)	306	0.71687	1	0.027827	1	0.91033	1	1	1	0.015371	1	0.0056384	1	0.0003553	0.162	0.11473	1
Del Peak  5(2q22.1)	78 (22%)	274	0.2975	1	0.0064758	1	0.29043	1	0.5224	1	0.051329	1	0.029155	1	0.090866	1	0.044006	1
Del Peak  6(2q36.2)	104 (30%)	248	5.4004e-08	2.78e-05	5.6852e-06	0.0028	0.11414	1	0.53143	1	0.00063648	0.285	0.0012545	0.541	0.0035977	1	0.23158	1
Del Peak  7(3p25.3)	247 (70%)	105	7.6657e-25	4.25e-22	2.9222e-10	1.55e-07	0.2132	1	0.38968	1	0.013367	1	0.063212	1	0.13747	1	0.00066436	0.296
Del Peak  8(3p14.2)	263 (75%)	89	2.4918e-29	1.4e-26	8.8083e-08	4.5e-05	0.25943	1	0.49976	1	0.11513	1	0.16112	1	0.5212	1	0.039397	1
Del Peak  9(3p14.2)	263 (75%)	89	2.4918e-29	1.4e-26	5.7076e-07	0.000289	0.21634	1	0.38638	1	0.11513	1	0.16112	1	0.5212	1	0.039397	1
Del Peak 10(3p12.2)	249 (71%)	103	6.7678e-29	3.78e-26	4.0436e-09	2.13e-06	0.85344	1	0.68385	1	0.24092	1	0.46324	1	0.30398	1	0.17824	1
Del Peak 11(4p15.2)	150 (43%)	202	3.0525e-12	1.65e-09	5.9825e-07	0.000302	0.048294	1	0.12972	1	0.040558	1	0.012897	1	0.0076867	1	0.62008	1
Del Peak 12(4q22.1)	117 (33%)	235	8.6717e-09	4.54e-06	6.4957e-07	0.000327	0.13025	1	0.65057	1	0.37116	1	0.2052	1	0.30053	1	0.67484	1
Del Peak 13(4q35.2)	145 (41%)	207	7.5109e-09	3.94e-06	2.9651e-05	0.0145	0.096178	1	0.53441	1	0.2748	1	0.35295	1	0.21612	1	0.46187	1
Del Peak 14(5q11.2)	142 (40%)	210	5.2732e-17	2.91e-14	1.3467e-12	7.3e-10	0.018553	1	0.6148	1	0.040089	1	0.00076743	0.34	0.069693	1	0.52235	1
Del Peak 15(5q35.3)	134 (38%)	218	7.2039e-18	3.98e-15	4.2509e-14	2.32e-11	0.41879	1	0.064507	1	0.014627	1	0.00047704	0.216	0.23123	1	0.7426	1
Del Peak 16(6p25.3)	68 (19%)	284	0.0019466	0.825	0.00033012	0.152	0.072714	1	0.13295	1	0.0075151	1	0.37979	1	0.11484	1	0.73961	1
Del Peak 17(7q31.1)	54 (15%)	298	0.00091832	0.403	0.026114	1	0.1704	1	0.58095	1	0.36345	1	0.60935	1	0.62379	1	0.42062	1
Del Peak 18(7q36.1)	86 (24%)	266	0.00018192	0.0848	0.33047	1	0.0051092	1	0.27657	1	0.9573	1	0.67433	1	0.86869	1	0.41862	1
Del Peak 19(8p23.2)	201 (57%)	151	2.1716e-15	1.19e-12	3.8374e-05	0.0186	0.13389	1	0.18778	1	0.016617	1	0.0035288	1	0.11667	1	0.05538	1
Del Peak 20(9p23)	161 (46%)	191	1.1576e-16	6.36e-14	5.4222e-09	2.85e-06	0.53765	1	0.85064	1	0.73968	1	0.49317	1	0.80244	1	0.72233	1
Del Peak 21(9p21.3)	204 (58%)	148	2.7068e-13	1.47e-10	2.8251e-09	1.49e-06	0.70654	1	0.42258	1	0.39019	1	0.46183	1	0.6975	1	0.61996	1
Del Peak 22(9q21.11)	65 (18%)	287	2.8637e-08	1.48e-05	0.00096226	0.421	0.95975	1	0.9265	1	0.88221	1	0.67272	1	0.70833	1	0.01115	1
Del Peak 23(9q34.3)	56 (16%)	296	0.0003331	0.153	0.031639	1	0.71183	1	0.10819	1	0.85073	1	0.40851	1	0.27527	1	0.086088	1
Del Peak 24(10p15.3)	114 (32%)	238	5.457e-06	0.00269	0.029339	1	0.5045	1	0.15506	1	0.32749	1	0.30691	1	0.26381	1	0.61935	1
Del Peak 25(10p11.21)	107 (30%)	245	9.7948e-06	0.00481	0.14501	1	0.22533	1	0.065174	1	0.70229	1	0.97498	1	0.54662	1	0.51881	1
Del Peak 26(10q23.31)	89 (25%)	263	1.5452e-06	0.000771	0.004161	1	0.17919	1	0.54795	1	0.024871	1	0.012786	1	0.037608	1	0.67334	1
Del Peak 27(11p15.4)	110 (31%)	242	1.5994e-08	8.32e-06	0.00052338	0.236	0.47097	1	0.45787	1	0.0022763	0.958	0.0070965	1	0.00092664	0.406	0.37457	1
Del Peak 28(11q14.1)	112 (32%)	240	4.774e-25	2.65e-22	0.085114	1	0.19297	1	0.76868	1	0.010529	1	0.036854	1	0.48462	1	0.55104	1
Del Peak 29(11q23.1)	169 (48%)	183	7.7044e-18	4.25e-15	8.4538e-07	0.000423	0.16922	1	0.25442	1	0.00081497	0.36	0.00023024	0.107	0.13173	1	0.27415	1
Del Peak 30(12q24.33)	40 (11%)	312	0.04272	1	0.064574	1	0.08201	1	0.74803	1	0.85888	1	0.77501	1	0.97659	1	0.34549	1
Del Peak 31(13q12.11)	159 (45%)	193	2.628e-11	1.41e-08	7.2846e-07	0.000366	0.27162	1	0.37108	1	0.053034	1	0.028941	1	0.47818	1	0.88899	1
Del Peak 32(13q14.2)	149 (42%)	203	2.8634e-06	0.00142	5.8809e-07	0.000298	0.15108	1	0.27524	1	5.702e-05	0.0274	6.4644e-05	0.0309	0.0085658	1	0.95356	1
Del Peak 33(14q11.2)	51 (14%)	301	0.00061346	0.275	0.0061601	1	0.3801	1	0.51483	1	0.46295	1	0.3287	1	0.064196	1	0.18476	1
Del Peak 34(14q32.32)	53 (15%)	299	0.026684	1	1.4205e-07	7.23e-05	0.098444	1	0.41296	1	0.00024216	0.112	9.7977e-05	0.0462	0.0012292	0.531	0.074433	1
Del Peak 35(15q15.1)	79 (22%)	273	0.0014049	0.601	0.77789	1	0.29349	1	0.16101	1	0.022578	1	0.062757	1	0.12582	1	0.26207	1
Del Peak 36(16q12.1)	62 (18%)	290	0.0092222	1	1.1258e-07	5.74e-05	0.74632	1	0.089598	1	7.1021e-08	3.64e-05	3.9142e-07	0.000199	0.00032957	0.152	0.011963	1
Del Peak 37(16q23.3)	72 (20%)	280	0.016727	1	0.00083917	0.37	0.50372	1	0.019585	1	0.00060143	0.27	8.8834e-05	0.042	0.01354	1	0.22313	1
Del Peak 38(17q25.3)	42 (12%)	310	0.47692	1	0.12256	1	0.4739	1	1	1	0.036979	1	0.061224	1	0.032151	1	0.076339	1
Del Peak 39(18q21.2)	182 (52%)	170	7.2668e-17	4e-14	1.6888e-09	8.92e-07	0.60301	1	0.64213	1	0.0026752	1	0.0072982	1	0.0021919	0.925	0.016978	1
Del Peak 40(18q23)	198 (56%)	154	8.5661e-20	4.75e-17	1.3766e-11	7.41e-09	0.18301	1	0.38539	1	0.0021609	0.914	0.0033283	1	0.0092432	1	0.038664	1
Del Peak 41(19p13.3)	117 (33%)	235	3.5657e-06	0.00177	0.036842	1	0.31002	1	0.081733	1	0.087593	1	0.76122	1	0.44236	1	0.30487	1
Del Peak 42(19q13.43)	68 (19%)	284	1.0335e-05	0.00506	6.9318e-05	0.0331	0.25553	1	0.084149	1	0.58361	1	0.26181	1	0.10173	1	0.68005	1
Del Peak 43(Xp21.3)	116 (33%)	236	4.3008e-05	0.0208	0.0053235	1	0.42445	1	0.06491	1	0.27514	1	0.041471	1	0.19964	1	0.37789	1
Del Peak 44(Xp11.3)	114 (32%)	238	4.6507e-06	0.0023	5.7969e-05	0.0278	0.34603	1	0.009136	1	0.211	1	0.059839	1	0.094733	1	0.97397	1
Del Peak 45(Xq21.33)	56 (16%)	296	0.0016762	0.714	0.0016593	0.709	0.025525	1	0.44409	1	0.0013088	0.561	0.012344	1	4.882e-05	0.0236	0.0041863	1