Table S2. Most frequent copy number aberrations in the optimal quality samples only (N=777).

Chr	Region ID	Loss Freq	Gain Freq	Start	End	Mb	Genes	cytoBands
1	13	1%	34%	145 394 955	148 544 968	3.0E+0	BCL9, TXNIP	q21.1–2
1	15	0%	35%	149 742 045	161 515 326	1.0E+1	MLLT11, NTRK1, PRCC, TPM3, PYHIN1, EFNA1, MUC1, PLEKHO1, AIM2	q21.2–q23.3
1	16	1%	32%	161 591 477	161 607 441	2.0E−2		q23.3
1	17	1%	34%	161 609 660	161 622 701	1.0E−2		q23.3
1	18	0%	32%	161 641 596	196 703 707	4.0E+1	FCGR2B, PBX1, TPR, LHX4, CDC73	q23.3–q31.3
3	65	3%	32%	143 794 370	151 504 070	8.0E+0	WWTR1	q24–q25.1
3	66	3%	33%	151 520 944	151 546 041	3.0E−2		q25.1
3	67	3%	34%	151 563 527	162 500 864	1.0E+1	CCNL1, GMPS	q25.1–q26.1
3	69	2%	34%	162 640 497	162 702 814	6.0E−2		q26.1
3	70	2%	34%	162 719 684	165 245 914	3.0E+0		q26.1
3	71	2%	34%	165 270 444	165 296 562	3.0E−2		q26.1
3	72	2%	35%	165 314 375	169 905 944	5.0E+0	MECOM	q26.1–2
3	73	2%	34%	169 918 311	175 861 931	6.0E+0	PRKCI, PRKCI	q26.2–32
3	74	2%	33%	175 889 230	175 905 626	2.0E−2		q26.32
3	75	2%	33%	175 920 884	187 866 388	1.0E+1	PIK3CA, DCUN1D1, BCL6	q26.32–q27.3
3	76	3%	33%	187 870 778	189 361 993	1.0E+0		q27.3–q28
3	77	3%	32%	189 365 570	189 367 551	2.0E−3		q28
3	78	3%	34%	189 370 963	195 341 037	6.0E+0		q28–q29
3	79	3%	34%	195 419 229	197 852 564	2.0E+0		q29
5	101	0%	47%	38 139	685 504	6.0E−1	SDHA	p15.33
5	102	1%	45%	718 972	766 213	5.0E−2		p15.33
5	103	0%	46%	776 473	8 685 711	8.0E+0	TERT	p15.33–31
5	104	0%	45%	8 704 021	8 737 812	3.0E−2		p15.31
5	105	0%	45%	8 753 733	17 516 734	9.0E+0		p15.31–p15.1
5	106	0%	45%	17 602 685	17 634 942	3.0E−2		p15.1
5	107	0%	44%	17 648 614	32 164 826	1.0E+1		p15.1–p13.3
5	108	0%	42%	32 168 437	45 893 362	1.0E+1	DAB2	p13.3–p12
5	109	1%	41%	45 895 885	45 915 513	2.0E−2		p12
5	110	1%	39%	45 939 674	46 381 782	4.0E−1		p12–p11
8	199	1%	32%	91 055 345	114 039 680	2.0E+1	RUNX1T1, TP53INP1	q21.3–q23.3
8	200	1%	32%	114 041 368	114 044 217	3.0E−3		q23.3
8	201	1%	34%	114 052 153	123 551 840	9.0E+0	EXT1	q23.3–q24.13
8	202	1%	37%	123 567 563	130 055 981	6.0E+0	MYC, MTSS1	q24.13–21
8	203	1%	36%	130 070 130	137 656 246	8.0E+0	WISP1	q24.21–23
8	204	2%	33%	137 693 433	137 855 026	2.0E−1		q24.23
8	205	1%	34%	137 862 600	146 114 526	8.0E+0	MAFA	q24.3–23
9	209	30%	4%	13 059 473	16 048 844	3.0E+0		p23–p22.3
9	213	30%	3%	21 785 018	21 845 577	6.0E−2		p21.3
9	214	31%	3%	21 853 221	22 176 560	3.0E−1	CDKN2A, CDKN2B	p21.3
9	215	30%	3%	22 202 151	23 953 634	2.0E+0		p21.3