Prediction of early-stage hepatocellular carcinoma using OncoScan chromosomal copy number aberration data

Table 1 Summary of chromosome imbalances in 120 hepatocellular carcinoma specimens and normal paired tissues

Chromosome region	Copy number	Cytoband	Grade I/II HCC	Grade III/IV HCC	P value
1q	Gain	1q21.1-44	57.86%	60.63%	NS
4q	Loss	4q13.1- 35.2	39.56%	47.51%	NS
8p	Loss	8p 23.2-21.1	48.56%	56.28%	NS
8q	Gain	8q12.3-24.3	39.99%	62.01%	0.006a
16q	Loss	16q23.3-24.3	38.96%	47.32%	NS
17p	Loss	17p13.3-12	52.22%	53.73%	NS
17q	Gain	17q22-25.3	37.76%	36.37%	NS

^aP < 0.05, statistically significant (Grade I/II vs Grade III/IV). NS: Not significant; HCC: Hepatocellular carcinoma.

Table 2 Disease-free survival analysis of clinicopathological data and percentage genome change of 120 patients with hepatocellular carcinoma

Clinicopathological factor	Log-rank test, P value	Cox regression analysis, P value	HR (95%CI)
Age (yr), ≤ 49 (22.5%) vs > 49 (77.5%)	0.004a	0.169	0.674 (0.384-1.183)
Sex (M/F), M (81.7%) vs F (19.3%)	0.146
Tumor size (cm), ≤ 4.5 (69.2%) vs > 4.5 (30.8%)	0.001a	0.012a	1.959 (1.160-3.309)
Satellite lesions (%), Yes (7.5%) vs No (92.5%)	0.088	0.013a	2.900 (1255-6.702)
Vascular invasion (%), Yes (28.3%) vs No (71.7%)	0.240
Grading I, II, III, IV (%), III & IV (43.3%) vs I & II (56.7%)	0.004a	0.063	1.626 (0.974-2.717)
Margin < 0.5 cm (%), ≤ 0.5 cm (47.5%) vs > 0.5 cm (52.5%)	0.210
Cirrhosis (%), Yes (54.2%) vs No (45.8%)	0.258
AFP (100 ng/mL), £100 (77.5%) vs > 100 (22.5%)	0.006a	0.462	1.244 (0.695-2.227)
Alkaline phosphatase (120 U/L), ≤ 120 (88.3%) vs > 120 (11.7%)	0.016a	0.042a	1.976 (1.025-3.808)
Staging I/II, II (40.0%) vs I (60.0%)	0.104
Percentage genome changed (60%), ≥ 60% (7.5%) vs < 60% (92.5%)	0.004a	0.031a	2.346 (1.080-5.097)

^aP < 0.05, statistically significant. AFP: α-fetoprotein; HCC: Hepatocellular carcinoma; HR: Hazard ratio; CI: Confidence interval; M: Male; F: Female.

Table 3 Cox regression analysis for disease-free survival in early-stage hepatocellular carcinoma

Gene	Cytoband	CNA	HR	95%CI	P value
ELAC2	17p12	Amplification	2.784	1.153-6.724	0.023a
MYC	8q24.21	Amplification	1.772	1.074-2.924	0.025a
SYK	9q22.2	Amplification	4.204	1.813-9.748	0.001a
GAK	4p16.3	Deletion	2.916	1.635-5.199	< 0.001a
MECOM	3q26.2	Deletion	5.932	2.012-17.489	0.001a
WRN	8p12	Deletion	1.9	1.172-3.080	0.009a

^aP < 0.05, statistically significant. HCC: Hepatocellular carcinoma; CNA: Copy number aberration; HR: Hazard ratio; CI: Confidence interval.