Table S9. Predictive effect of the copy number of genomic regions. Univariate results in optimal quality samples only.

Chr	Region ID	CNA frequency			Disease-free survival					Overall survival					Lung-cancer specific survival				Mb	Genes	cytoBands
		Losses	Gains		HR for loss* (95% CI)	HR for gain** (95% CI)	P	Q		HR for loss* (95% CI)	HR for gain** (95% CI)	P	Q		HR for loss* (95% CI)	HR for gain** (95% CI)	P	Q
5	102	0.6%	45.3%							0.45 (0.22–0.88)	2.2 (1.1–4.4)	0.021	0.705						5.0E−2		p15.33
9	232	17.2%	2.4%		4.0 (1.2–14)	0.25 (0.07–0.85)	0.026	0.979											2.0E+1		q21.11–q22.1
	233	15.6%	3.2%		4.1 (1.2–14)	0.25 (0.07–0.84)	0.025	0.979											5.0E+0	FAM120A	q22.1–31
10	238	7.2%	4.6%							0.22 (0.06–0.82)	4.6 (1.2–17)	0.024	0.705						4.0E+0	RET, RASSF4	q11.21–22
14	318	8.9%	10.0%		0.29 (0.11–0.75)	3.4 (1.3–8.8)	0.010	0.979							0.22 (0.08–0.62)	4.5 (1.6–13)	0.004	0.614	2.0E−2		q32.33
	319	10.8%	11.4%		0.37 (0.17–0.81)	2.7 (1.2–6.0)	0.013	0.979											1.0E−1		q32.33
	325	16.3%	8.3%		0.66 (0.45–0.95)	1.5 (1.0–2.2)	0.028	0.979											3.0E−2		q32.33
	299	13.5%	9.4%							0.33 (0.13–0.83)	3.0 (1.2–7.6)	0.019	0.705						5.0E−1		q11.2
	302	6.4%	9.5%							0.29 (0.10–0.84)	3.4 (1.2–9.8)	0.022	0.705						4.0E+0		q11.2–q12
17	360	2.1%	14.2%							0.23 (0.07–0.82)	4.3 (1.2–15)	0.023	0.705						8.0E−2		q25.3
20	408	0.8%	20.8%												0.19 (0.06–0.63)	5.3 (1.6–18)	0.007	0.614	5.0E−1		q11.21
	409	0.8%	20.2%												0.19 (0.06–0.65)	5.3 (1.5–18)	0.008	0.614	1.0E−1		q11.21
	411	3.0%	17.4%												0.18 (0.05–0.60)	5.7 (1.7–19)	0.006	0.614	7.0E+0	SRC, MAFB, RBL1, MAFB	q11.22–q12
	412	3.1%	17.5%												0.21 (0.07–0.68)	4.7 (1.5–15)	0.009	0.614	3.0E−2		q12

Results from a model adjuster by treatment arm, patient age, sex, performance status (PS), histology, T, and N stage. *, hazard ratio for a 2-fold lower copy number; **, hazard ratio for a 2-fold higher copy number.