Clinical Features	CN_CNMF		METHLYATION_CNMF		MRNASEQ_CNMF		MRNASEQ_CHIERARCHICAL		MIRSEQ_CNMF		MIRSEQ_CHIERARCHICAL	
	nCNV (%)	nWild-Type	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
1p gain	3 (2%)	188	0.56012	0.742	0.33603	0.555	0.26082	0.486	0.58815	0.758	0.00105	0.0194	0.091859	0.245
4p gain	4 (2%)	187	0.03593	0.128	0.02586	0.108	NA	NA	NA	NA	0.59245	0.758	0.8347	0.96
4q gain	4 (2%)	187	0.03541	0.128	0.0265	0.108	NA	NA	NA	NA	0.59251	0.758	0.83268	0.96
8p gain	22 (12%)	169	0.95942	1	0.00223	0.0268	0.02733	0.109	0.00075999	0.0171	0.068319	0.212	0.01652	0.0835
8q gain	23 (12%)	168	0.88574	0.989	0.0055799	0.045	0.01413	0.08	0.00182	0.0233	0.061849	0.198	0.01416	0.08
10q gain	3 (2%)	188	0.44715	0.645	0.33746	0.555	0.26243	0.486	0.58694	0.758	0.15926	0.361	0.092979	0.245
11p gain	5 (3%)	186	0.44324	0.645	0.30593	0.523	0.23068	0.452	0.23452	0.452	0.01514	0.0807	0.03214	0.122
11q gain	7 (4%)	184	0.23306	0.452	0.072799	0.221	0.076739	0.223	0.074749	0.221	0.00177	0.0233	0.01505	0.0807
13q gain	6 (3%)	185	0.42251	0.629	0.02377	0.101	0.14883	0.345	0.083249	0.235	0.00182	0.0233	0.073609	0.221
17q gain	3 (2%)	188	0.79508	0.925	0.78265	0.925	1	1	0.589	0.758	0.66355	0.827	0.30313	0.523
19p gain	5 (3%)	186	0.39919	0.62	0.26471	0.486	1	1	0.86476	0.972	0.40874	0.62	1	1
19q gain	5 (3%)	186	0.39736	0.62	0.26664	0.486	1	1	0.86577	0.972	0.41044	0.62	1	1
21q gain	8 (4%)	183	0.12603	0.31	0.21542	0.445	0.14917	0.345	0.5251	0.725	0.04981	0.165	0.40866	0.62
22q gain	9 (5%)	182	0.2394	0.455	0.01209	0.0749	0.14778	0.345	0.01629	0.0835	0.00066999	0.0171	0.01356	0.08
xp gain	3 (2%)	188	0.79426	0.925	0.47946	0.672	NA	NA	NA	NA	0.4429	0.645	0.04605	0.159
xq gain	3 (2%)	188	0.7945	0.925	0.47791	0.672	NA	NA	NA	NA	0.44228	0.645	0.04703	0.159
3p loss	3 (2%)	188	0.02271	0.101	0.33799	0.555	0.7865	0.925	1	1	0.10107	0.255	0.092149	0.245
3q loss	3 (2%)	188	0.02172	0.101	0.3358	0.555	0.7848	0.925	1	1	0.10074	0.255	0.093209	0.245
5q loss	6 (3%)	185	0.30207	0.523	0.02229	0.101	0.22841	0.452	0.63166	0.795	0.03251	0.122	0.03203	0.122
7p loss	17 (9%)	174	9.9999e-06	0.000384	0.00042	0.0134	0.00111	0.0194	9.9999e-06	0.000384	0.0065799	0.0486	0.00293	0.0316
7q loss	20 (10%)	171	9.9999e-06	0.000384	9.9999e-06	0.000384	0.0097799	0.0626	9.9999e-06	0.000384	0.00296	0.0316	0.00079999	0.0171
12p loss	4 (2%)	187	0.53753	0.728	0.50184	0.698	0.38057	0.614	0.38864	0.62	0.39792	0.62	0.18443	0.392
15q loss	4 (2%)	187	0.53862	0.728	0.45045	0.645	0.096799	0.251	0.36913	0.601	0.1426	0.345	0.1853	0.392
16q loss	4 (2%)	187	0.03571	0.128	0.16066	0.361	0.78853	0.925	1	1	0.02372	0.101	0.02299	0.101
17p loss	13 (7%)	178	0.01712	0.0843	0.00356	0.0344	0.17095	0.377	0.00157	0.0233	0.19487	0.407	0.00358	0.0344
17q loss	7 (4%)	184	0.085819	0.239	0.14857	0.345	0.078179	0.224	0.23565	0.452	0.11898	0.297	0.04706	0.159
18p loss	5 (3%)	186	0.0090899	0.0626	0.064669	0.204	1	1	0.86487	0.972	0.26854	0.486	0.185	0.392
18q loss	4 (2%)	187	0.53778	0.728	0.16181	0.361	0.47539	0.672	0.86369	0.972	0.061659	0.198	0.18567	0.392
19p loss	3 (2%)	188	0.56036	0.742	0.78349	0.925	0.78711	0.925	1	1	0.28269	0.503	0.41306	0.62
19q loss	3 (2%)	188	0.55918	0.742	0.78264	0.925	0.7871	0.925	1	1	0.28293	0.503	0.41308	0.62
xp loss	5 (3%)	186	0.0092599	0.0626	0.30788	0.523	0.22986	0.452	0.63321	0.795	0.0056299	0.045	0.0050399	0.044
xq loss	5 (3%)	186	0.0094499	0.0626	0.30661	0.523	0.22812	0.452	0.63091	0.795	0.0059799	0.0459	0.00495	0.044