Novel approach to identifying the hepatitis B virus pre-S deletions associated with hepatocellular carcinoma

Table 1 Characteristics of the 19 cases used for clone sequencing

Cases	Sex	Age	Clinical diagnosis	Clone No.	Pre-S deletion size (bp)	Pre-S deletion site (nt)
486	Male	33	HCC	486-1, 486-2, 486-3, 486-4, 486-5, 486-6	0	/
6-200	Male	60	HCC	6-200-1,6-200-2,6-200-3,6-200-4,6-200-5,6-200-6	0	/
440	Male	52	HCC	440-1, 440-2, 440-3, 440-4, 440-5, 440-6	6	6-11
221	Male	38	HCC	221-1	0	/
				221-2, 221-3, 221-4, 221-5, 221-6	78	3107-3184
644	Male	53	HCC	644-1, 644-2, 644-3, 644-5, 644-6	0	/
				644-4	33	18-50
606	Male	41	HCC	606-1, 606-2, 606-3, 606-4, 606-6	0	/
				606-5	3	3199-3201
6-133	Male	50	HCC	6-133-1, 6-133-3, 6-133-4, 6-133-5	0	/
				6-133-2, 6-133-6	42	25-66
4-066	Female	58	HCC	4-066-1, 4-066-2, 4-066-4, 4-066-5, 4-066-6	0	/
				4-066-3	33	34-66
140	Male	64	CH	140-1, 140-2, 140-3, 140-4, 140-5, 140-6	0	/
79	Female	45	CH	79-1, 79-2, 79-3, 79-4, 79-5, 79-6	0	/
96	Male	43	CH	96-1, 96-2, 96-3, 96-4, 96-5, 96-6	0	/
141	Male	32	CH	141-1, 141-2, 141-3, 141-4, 141-5, 141-6	0	/
207	Male	60	CH	207-1, 207-2, 207-3, 207-4, 207-5, 207-6	36	62-97
259	Male	70	CH	259-1, 259-2, 259-3, 259-4, 259-5, 259-6	183	3015-3197
70	Male	49	CH	70-1, 70-5	126	2970-3095
				70-2, 70-3, 70-4, 70-6	0	/
296	Male	56	CH	296-1, 296-4, 296-5, 296-6	0	/
				296-2, 296-3	123	2922-3044
356	Male	38	CH	356-1, 356-4, 356-5, 356-6	0	/
				356-2	21	33-53
				356-3	54	2906-2959
229	Male	67	CH	229-1, 229-6	15	42-56
				229-2, 229-3, 229-4, 229-5	0	/
322	Male	58	CH	322-1. 322-2, 322-3, 322-4, 322-6	0	/
				322-5	24	45-68

HCC: Hepatocellular carcinoma.

Table 2 Comparison of cloning-based sequencing and capillary gel electrophoresis analysis of HBV pre-S deletions

Size of deletion (bp)	Cloning-based sequencing (No.)	Capillary gel electrophoresis1 (No.)
Wild type	77	77
Pre-S deletion
0-51	21	20
54-99	6	6
102-294	10	10
Total	114	113

¹The number of clones for which the result was in agreement with that of the sequencing analysis.

Table 3 Analysis of pre-S deletions in hepatocellular carcinoma and non- hepatocellular carcinoma patients by capillary gel electrophoresis n (%)

Characteristics	HCCn = 157	Non-HCCn = 160	P value	OR (95%CI)
Age range, yr
≤ 48	78 (49.7)	88 (55.0)	0.343
> 48	79 (50.3)	72 (45.0)		/
Gender
Male	136 (86.6)	133 (83.1)	0.385	/
Female	21 (13.4)	27 (16.9)		/
Mutation pattern
Pre-S deletion alone	22 (14.0)	11 (6.9)	0.037	2.207 (1.032-4.722)
Wild type + deletion	52 (33.1)	34 (21.2)	0.017	1.835 (1.109-3.038)
Total deletions	74 (47.1)	45 (28.1)	< 0.001	2.278 (1.430-3.630)

HCC: Hepatocellular carcinoma.

Table 4 Analysis of the correlation between the size of pre-S deletion and hepatocellular carcinoma n (%)

Characteristics	HCCn = 157	Non-HCCn = 160	P value	OR (95%CI)
Wild type	83 (52.9%)	115 (71.9%)
Pre-S deletion
Deletion ≤ 99 bp	54 (34.4%)	24 (15.0%)	< 0.001	2.971 (1.723-5.122)
Deletion > 99 bp	20 (12.7%)	21 (13.1%)	0.918	0.966 (0.501-1.863)