Table 3. Copy number and outcome.

Event-free survival (EFS) and overall survival (OS) are displayed for the recurring regions and other commonly reported CNAs in Ewing sarcoma. Both adjusted and unadjusted P values are displayed. Outcome is adjusted for age at diagnosis greater than 10 years and the presence of metastatic disease at diagnosis. The regions on Chromosome 20q remain significant after adjustment and therefore have the strongest independent correlation with clinical outcome.

	EVENT FREE SURVIVAL (N=40)						OVERALL SURVIVAL (N=40)

Alteration	Gain or Loss Present		No gain or Loss		P-value (unadjusted)	P-value (adjusted)	Gain or Loss Present		No gain or Loss		P-value (unadjusted)	P-value (adjusted)

	Relapse or Death	5-year survival	Relapse or Death	5-year survival			Death	5-year survival	Death	5-year survival
	Relapse or Death	(95% CI)	Relapse or Death	(95% CI)			Death	(95% CI)	Death	(95% CI)
1q amplification	1/7	0.8	11/33	0.59	0.33	0.68	0/7	1	8/33	0.64	0.14	0.33
1q amplification	1/7	(0.52–1.00)	11/33	(0.43–0.82)	0.33	0.68	0/7	1	8/33	(0.46–0.89)	0.14	0.33

Trisomy 5	3/3	0	9/37	0.7	0.01^*	0.54	3/3	0	5/37	0.81	0.0027^**	0.22
Trisomy 5	3/3	0	9/37	(0.56–0.89)	0.01^*	0.54	3/3	0	5/37	(0.67–0.98)	0.0027^**	0.22

MYC amplification	8/16	0.35	4/24	0.8	0.0059^**	0.58	8/16	0.26	0/24	1	0.0000174^***	---^&
MYC amplification	8/16	(0.16–0.80)	4/24	(0.64–1.00)	0.0059^**	0.58	8/16	(0.08–0.77)	0/24	1	0.0000174^***	---^&

Trisomy 8	7/15	0.38	5/25	0.77	0.032^*	0.95	7/15	0.28	1/25	0.96	0.00038^***	0.12
Trisomy 8	7/15	(0.17–0.84)	5/25	(0.61–0.97)	0.032^*	0.95	7/15	(0.09–0.92)	1/25	(0.88–1.00)	0.00038^***	0.12

CDKN2A deletion	0/2	1	12/38	0.61	0.39	---^&	0/2	1	8/38	0.7	0.66	---^&
CDKN2A deletion	0/2	1	12/38	(0.46–0.82)	0.39	---^&	0/2	1	8/38	(0.55–0.90)	0.66	---^&

Trisomy 12	2/5	0.5	10/35	0.66	0.85	0.35	2/5	0.38	6/35	0.76	0.43	0.65
Trisomy 12	2/5	(0.19–1.00)	10/35	(0.51–0.86)	0.85	0.35	2/5	(0.08–1.00)	6/35	(0.61–0.95)	0.43	0.65

16q24.1 deletion	4/5	0.2	8/35	0.73	0.041^*	0.65	3/5	0.4	5/35	0.79	0.1	0.77
16q24.1 deletion	4/5	(0.035–1.00)	8/35	(0.58–0.91)	0.041^*	0.65	3/5	(0.14–1.00)	5/35	(0.64–0.98)	0.1	0.77

16q23.3-24.1 deletion	4/5	0.2	8/35	0.72	0.014^*	0.31	3/5	0.4	5/35	0.77	0.03^*	0.13
16q23.3-24.1 deletion	4/5	(0.035–1.00)	8/35	(0.57–0.91)	0.014^*	0.31	3/5	(0.14–1.00)	5/35	(0.60–0.97)	0.03^*	0.13

16q deletion	3/4	0.25	9/36	0.7	0.11	0.68	2/4	0.5	6/36	0.74	0.26	0.47
16q deletion	3/4	(0.046–1.00)	9/36	(0.55–0.89)	0.11	0.68	2/4	(0.19–1.00)	6/36	(0.58–0.95)	0.26	0.47

20q13.2 amplification	4/7	0.26	8/33	0.7	0.00033^***	0.0084^**	4/7	0	4/33	0.81	0.00000019^***	0.0021^*
20q13.2 amplification	4/7	(0.053–1.00)	8/33	(0.54–0.90)	0.00033^***	0.0084^**	4/7	0	4/33	(0.66–0.99)	0.00000019^***	0.0021^*

*20q13.13 (CEBPB)* amplification**	3/6	0.3	9/34	0.68	0.012^*	0.07	3/6	0	5/34	0.79	0.00013^***	0.029^*
*20q13.13 (CEBPB)* amplification**	3/6	(0.063–1.00)	9/34	(0.52–0.88)	0.012^*	0.07	3/6	0	5/34	(0.63–0.98)	0.00013^***	0.029^*

Trisomy 20 (includes partial)	3/7	0.3	9/33	0.68	0.012^*	0.07	3/7	0	5/33	0.79	0.00013^***	0.029^*
Trisomy 20 (includes partial)	3/7	(0.063–1.00)	9/33	(0.52–0.88)	0.012^*	0.07	3/7	0	5/33	(0.63–0.98)	0.00013^***	0.029^*

Trisomy 21	2/4	0.5	10/36	0.64	0.41	0.58	2/4	0.5	6/36	0.74	0.2	0.96
Trisomy 21	2/4	(0.19–1.00)	10/36	(0.48–0.86)	0.41	0.58	2/4	(0.19–1.00)	6/36	(0.58–0.95)	0.2	0.96

INI1 deletion/loss of heterozygosity	0/3	1	12/37	0.59	0.21	---^&	0/3	1	8/37	0.67	0.28	---^&
INI1 deletion/loss of heterozygosity	0/3	1	12/37	(0.43–0.81)	0.21	---^&	0/3	1	8/37	(0.50–0.90)	0.28	---^&

Multifactor Copy Number (MCN)- Index	9/19	0.4	3/21	0.83	0.013^*	0.61	8/19	0.39	0/21	1	0.00059^***	0.047^*
Multifactor Copy Number (MCN)- Index	9/19	(0.21–0.78)	3/21	(0.67–1.00)	0.013^*	0.61	8/19	(0.19–0.80)	0/21	NA	0.00059^***	0.047^*

P<0.05,

^**

P<0.01,

^***

P<0.001,

Stratified Cox model did not converge.