Basic Study
Copyright ©The Author(s) 2017.
World J Gastroenterol. Jan 14, 2017; 23(2): 232-241
Published online Jan 14, 2017. doi: 10.3748/wjg.v23.i2.232
Table 1 Primer sequences and reaction conditions for genotyping APOBEC3G polymorphisms
SNPSequences of the primersAnnealing temperature, °C
Rs7291971F: 5’-ACGTTGGATGGATCATCTGAGGTCAGTGTC-3’59.6
R: 5’-ACGTTGGATGCCATCTGGATGTATATGTGC-3’
Rs5757465F: 5’-ACGTTGGATGTGTACAAGGGATATGGCCAC-3’54.6
R: 5’-ACGTTGGATGAATCTGGGTCCCAGAAGTAG-3’
Rs5757463F: 5’-ACGTTGGATGTAATTTGTAGGTCACCACGC-3’50.9
R: 5’-ACGTTGGATGAGCCTGTCTGGAGCCTCCCT-3’
Rs8177832F: 5’-ACGTTGGATGGAGCCTTGGAATAATCTGCC-3’51.5
R: 5’-ACGTTGGATGGAGACCCTCACCTGAGAATC-3’
Rs2011861F: 5’-ACGTTGGATGTCTTTTCCCGCAGGATGAAG-3’55.7
R: 5’-ACGTTGGATGATTTGAGGATCAGGGCCTAC-3’
Table 2 Baseline characteristics of study subjects, n (%)
GroupHealthy controls,Chronic HBV infection patients
P value3
n = 299Non-HCC
HBV-related HCC
n = 370P value1n = 287P value2
Male247 (82.6)295 (79.7)0.345246 (85.7)0.3040.921
Age, M (P25, P75)50 (45, 55)49 (42, 55)0.07850 (46, 56)0.5890.408
Smoking0.3920.0030.292
Ever113 (37.8)128 (34.6)144 (50.2)
Never186 (62.2)242 (65.4)143 (49.8)
Drinking0.0360.8040.241
Ever122 (40.8)122 (33.0)120 (41.8)
Never177 (59.2)248 (67.0)167 (58.2)
Table 3 Genotype and allele frequencies of single nucleotide polymorphisms in the APOBEC3G gene in each group
SNPHealthy controlsChronic HBV infection patients
Hepatitis B patients (n = 657) vs healthy controls (n = 299)
Non-HCC, n = 370
HBV-related HCC, n = 287
n = 299 (%)n (%)OR (95%CI)P value1n (%)OR (95%CI)P value2OR (95%CI)P value3
Rs7291971 genotype and allele
Detected numbern = 290n = 366n = 282n = 648 vs n = 290
CC28 (9.7)36 (9.8)126 (9.2)11
CG113 (39.0)139 (38.0)0.92 (0.53-1.61)0.778114 (40.4)1.14 (0.63-2.09)0.6671.00 (0.61-1.66)0.987
GG149 (51.4)191 (52.2)0.98 (0.57-1.68)0.935142 (50.4)1.14 (0.63-2.06)0.6641.04 (0.64-1.69)0.891
CG + GG2623300.95 (0.57-1.61)0.8672561.14 (0.65-2.02)0.6511.02 (0.64-1.64)0.930
C allele169 (29.1)211 (28.8)1166 (29.4)11
G allele411 (70.9)521 (71.2)1.02 (0.80-1.29)0.901398 (29.1)0.99 (0.76-1.27)0.9131.00 (0.80-1.24)0.983
Rs5757463 genotype and allele
Detected numbern = 285n = 369n = 285n = 654 vs n = 285
CC241 (84.6)308 (83.5)1227 (79.6)11
CG43 (15.1)56 (15.2)1.02 (0.66-1.57)0.94453 (18.6)1.34 (0.86-2.10)0.2021.16 (0.79-1.71)0.456
GG1 (0.4)5 (1.4)1.93 (0.37-10.14)0.4395 (1.8)2.71 (0.51-14.31)0.2392.25 (0.49-10.39)0.298
CG + GG44611.06 (0.69-1.62)0.799581.40 (0.91-2.17)0.1301.21 (0.83-1.77)0.327
C allele525 (92.1)672 (91.1)1507 (88.9)11
G allele45 (7.9)66 (8.9)1.15 (0.77-1.70)0.50063 (11.1)1.45 (0.97-2.17)0.0691.28 (0.90-1.82)0.194
Rs5757465 genotype and allele
Detected numbern = 285n = 365n = 279n = 644 vs n = 285
TT170 (59.6)221 (60.5)1169 (60.6)11
TC101 (35.4)129 (35.3)1.02 (0.73-1.42)0.89892 (33.0)0.93 (0.65-1.34)0.7070.98 (0.73-1.32)0.903
CC14 (4.9)15 (4.1)0.82 (0.38-1.76)0.61018 (6.5)1.43 (0.68-3.01)0.3491.05 (0.55-2.020.884
TC + CC1151440.99 (0.72-1.37)0.9841100.99 (0.70-1.39)0.9530.99 (0.74-1.320.945
T allele441 (77.4)571 (78.2)1430 (77.1)11
C allele129 (22.6)159 (21.8)0.95 (0.73-1.24)0.714128 (22.9)1.02 (0.77-1.34)0.9020.98 (0.77-1.24)0.868
Rs8177832 genotype and allele
Detected numbern = 291n = 369n = 287n = 656 vs n = 291
AA227 (78.0)302 (81.8)1249 (86.8)11
AG60 (20.6)65 (17.6)0.80 (0.54-1.18)0.25335 (12.2)0.53 (0.33-0.84)0.0070.67 (0.47-0.96)0.029
GG4 (1.4)2 (0.5)0.40 (0.72-2.26)0.3023 (1.0)0.75 (0.16-3.43)0.7110.55 (0.15-2.07)0.374
AG + GG64670.78 (0.53-1.14)0.195380.54 (0.35-0.85)0.0070.66 (0.47-0.94)0.021
A allele514 (88.3)669 (90.7)1533 (92.9)11
G allele68 (11.7)69 (9.3)0.78 (0.55-1.11)0.16741 (7.1)0.58 (0.39-0.87)0.0080.69 (0.50-0.95)0.023
Rs2011861 genotype and allele
Detected numbern = 284n = 364n = 279n = 643 vs n = 284
CC53 (18.7)55 (15.1)133 (11.8)11
CT127 (44.7)170 (46.7)1.25 (0.80-1.95)0.328135 (48.4)1.69 (1.02-2.80)0.0421.42 (0.95-2.13)0.085
TT104 (36.6)139 (38.2)1.27 (0.81-2.02)0.301111 (39.8)1.82 (1.08-3.06)0.0241.48 (0.98-2.24)0.063
CT + TT2313091.26 (0.83-1.91)0.2772461.75 (1.08-2.82)0.0221.45 (0.99-2.11)0.053
C allele233 (41.0)280 (38.5)1201 (36.0)11
T allele335 (59.0)448 (61.5)1.11 (0.89-1.39)0.350357 (64.0)1.24 (0.97-1.57)0.0851.16 (0.95-1.42)0.140
Table 4 Haplotype distributions between healthy controls and chronic hepatitis B virus infection patients, n (%)
HaplotypeFrequency
χ2P valueOR (95%CI)
Healthy controlsChronic HBV infection patients
rs5757463-rs8177832
C-A455 (80.3)1067 (81.7)6.070.0481
C-G66 (11.7)110 (8.4)0.71 (0.51-0.98)
G-A45 (8.0)129 (9.9)1.22 (0.86-1.75)
Table 5 Haplotype distributions between healthy controls and hepatocellular carcinoma patients, n (%)
HaplotypeFrequency
χ2P valueOR (95%CI)
Healthy controlsHCC
rs7291971-rs8177832
C-A166 (29.0)166 (29.4)6.730.031
G-A339 (59.3)357 (63.3)1.05 (0.81-1.37)
G-G67 (11.7)41 (7.3)0.61 (0.39-0.95)
rs5757463-rs8177832
C-A455 (80.4)466 (81.8)8.960.011
C-G66 (11.7)41 (7.2)0.61 (0.40-0.91)
G-A45 (8.0)63 (11.1)1.37 (0.91-2.05)
rs5757465-rs8177832
T-A371 (66.0)390 (69.9)6.940.031
C-A125 (22.2)128 (22.9)0.97 (0.73-1.30)
T-G66 (11.7)40 (7.2)0.58 (0.38-0.88)
rs5757463-rs2011861
C-C183 (33.2)141 (25.4)10.680.011
C-T326 (59.1)354 (63.7)1.41 (1.08-1.83)
G-C43 (7.8)60 (10.8)1.80 (1.15-2.82)
G-T0 (0.0)1 (0.2)1.00 (0.99-1.02)
rs7291971-rs5757463-rs8177832
C-C-A118 (21.1)101 (18.0)10.590.011
C-G-A45 (8.0)63 (11.3)1.64 (1.03-2.61)
G-C-A332 (59.3)355 (63.4)1.25 (0.92-1.70)
G-C-G65 (11.6)41 (7.3)0.74 (0.46-1.18)
rs7291971-rs5757463-rs2011861
C-C-C112 (20.4)91 (16.6)11.620.041
C-C-T5 (0.9)6 (1.1)1.63 (0.42-6.42)
C-G-C43 (7.8)59 (10.8)1.70 (1.05-2.76)
C-G-T0 (0.0)2 (0.4)1.02 (0.99-1.05)
G-C-C70 (12.8)48(8.8)0.85 (0.85-1.35)
G-C-T319 (58.1)342 (62.4)1.33 (0.97-1.82)