| Literature DB >> 26538132 |
De-Ke Jiang1,2,3,4,5,6, Xiao-Pin Ma1, Xiaopan Wu7, Lijun Peng8, Jianhua Yin9, Yunjie Dan10, Hui-Xing Huang1, Dong-Lin Ding1, Lu-Yao Zhang1, Zhuqing Shi1,2,3,4, Pengyin Zhang1,2,3,4, Hongjie Yu1,2,3,4, Jielin Sun5, S Lilly Zheng5,6, Guohong Deng10, Jianfeng Xu1,2,3,4,5,6,11, Ying Liu7, Jinsheng Guo8, Guangwen Cao9, Long Yu1,12.
Abstract
Recent genome-wide associated studies (GWASs) have revealed several common loci associated with the risk of hepatitis B virus (HBV)- or hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC). We selected 15 single nucleotide polymorphisms (SNPs) identified through GWASs on HBV- or HCV-related HCC, and genotyped them in two independent Chinese cohorts of chronic HBV carriers, including 712 LC cases and 2601 controls. The association of each SNP with the risk of HBV-related LC was assessed by meta-analysis of the two cohorts. Of the 12 SNPs reported in HBV-related HCC GWASs, five SNPs (rs7574865 in STAT4, rs9267673 near C2, rs2647073 and rs3997872 near HLA-DRB1 and rs9275319 near HLA-DQ), were found to be significantly associated with the risk of HBV-related LC (rs7574865: P = 1.79 × 10(-2), OR = 1.17, 95% CI = 1.03-1.34; rs9267673: P = 4.91 × 10(-4), OR = 1.37, 95% CI = 1.15-1.63; rs2647073: P = 3.53 × 10(-5), OR = 1.63, 95% CI = 1.29-2.06; rs3997872: P = 4.22 × 10(-4), OR = 1.86, 95% CI = 1.32-2.62; rs9275319: P = 1.30 × 10(-2), OR = 1.32, 95% CI = 1.06-1.64). However, among the three SNPs associated with the risk of HCV-related HCC in previous GWASs, none of them showed significant association with the risk of HBV-related LC. Our results suggested that genetic variants associated with HBV-related hepatocarcinogenesis may already play an important role in the progression from CHB to LC.Entities:
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Year: 2015 PMID: 26538132 PMCID: PMC4633722 DOI: 10.1038/srep16278
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Demographic characteristics of subjects analyzed in the study.
| Subjects | Number | Gender, n (%) | Age, years | |||
|---|---|---|---|---|---|---|
| Female | Male | Mean (SD) | ≤50, n (%) | >50, n (%) | ||
| Shanghai cohort | ||||||
| Cases | 440 | 109 (24.77) | 331 (75.23) | 49.53 (10.94) | 249 (56.59) | 191 (43.41) |
| Controls | 1265 | 464 (36.68) | 801 (63.32) | 51.00 (12.89) | 536 (42.47) | 729 (57.63) |
| Beijing cohort | ||||||
| Cases | 272 | 65 (23.90) | 207 (76.10) | 48.19 (12.30) | 160 (58.82) | 112 (41.18) |
| Controls | 1336 | 491 (36.75) | 845 (63.25) | 42.73 (15.04) | 947 (70.88) | 389 (29.12) |
aRecruited from Shanghai in eastern China.
bRecruited from Beijing in northern China.
Information of the SNPs previously reported to be associated with the risk of HBV- and HCV-related HCC by GWASs.
| Chr. | Related gene | Distance to gene | Position | SNP | Allele | Risk allele | RAF in CHB | Ref. |
|---|---|---|---|---|---|---|---|---|
| 1 | Intron 24 | 10308058 | rs17401966 | G/A | A | 0.733 | ||
| 2 | Intron 3 | 191672878 | rs7574865 | T/G | G | 0.650 | ||
| 3 | 18 kb upstream | 32995039 | rs4678680 | G/T | G | 0.037 | ||
| 6 | 12 kb upstream | 31991658 | rs9267673 | T/C | T | 0.159 | ||
| 6 | 16 kb downstream | 32681992 | rs2647073 | C/A | C | 0.098 | ||
| 6 | 23 kb downstream | 32688595 | rs3997872 | A/T | A | 0.037 | ||
| 6 | 96kb downstream of HLA-DQA1 | 32707977 | rs9272105 | G/A | A | 0.524 | ||
| 6 | 42 kb downstream of HLA-DQB2 | 32774273 | rs9275319 | G/A | A | 0.783 | ||
| 6 | Intron 5 | 90791705 | rs7749730 | G/A | A | 0.890 | ||
| 8 | — | — | 37548149 | rs12682266 | A/G | G | 0.488 | |
| 14 | Intron 5 | 89370788 | rs12100561 | A/G | A | 0.366 | ||
| 21 | Intron 1 | 30068040 | rs455804 | A/C | C | 0.683 | ||
| 6 | 4.7 kb upstream | 31474574 | rs2596542 | T/C | T | 0.256 | ||
| 6 | Intron 1 | 32786977 | rs9275572 | A/G | A | 0.317 | ||
| 22 | Intron 32 | 30595903 | rs1012068 | G/T | G | 0.134 |
Chr. chromosome; RAF, risk allele frequency; CHB, Chinese Han in Beijing from in HapMap.
aMinor allele/major allele.
bRisk allele means the allele associated with increased risk of HBV-related HCC in the original GWAS.
CAllele frequency in CHB+JPT in HapMap.
Results of association between SNPs previously reported by HBV-related HCC GWAS and the risk of progression from CHB to LC.
| Gene | SNP | Allele | RAF | RAF | ORmeta (95% CI) | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Cases | Controls | Cases | Controls | |||||||
| rs17401966 | G/A | 0.33 | 0.29 | 0.28 | 0.28 | 1.13 (0.99–1.30) | 8.03 × 10−2 | 1.64 × 10−1 | 0.522 | |
| rs7574865 | T/G | 0.72 | 0.67 | 0.72 | 0.69 | 1.17 (1.03–1.34) | 1.79 × 10−2 | 4.18 × 10−2 | 0.894 | |
| rs4678680 | G/T | 0.94 | 0.93 | 0.92 | 0.93 | 1.13 (0.87–1.47) | 3.45 × 10−1 | 4.57 × 10−1 | 0.958 | |
| rs9267673 | T/C | 0.17 | 0.12 | 0.13 | 0.12 | 1.37 (1.15–1.63) | 4.91 × 10−4 | 1.74 × 10−3 | 0.680 | |
| rs2647073 | C/A | 0.09 | 0.05 | 0.10 | 0.08 | 1.63 (1.29–2.06) | 3.53 × 10−5 | 3.75 × 10−4 | 0.886 | |
| rs3997872 | A/T | 0.97 | 0.94 | 0.97 | 0.95 | 1.86 (1.32–2.62) | 4.22 × 10−4 | 1.66 × 10−3 | 0.997 | |
| rs9272105 | A/G | 0.43 | 0.41 | 0.42 | 0.39 | 1.07 (0.95–1.20) | 2.59 × 10−1 | 3.87 × 10−1 | 0.981 | |
| rs9275319 | G/A | 0.91 | 0.89 | 0.93 | 0.90 | 1.32 (1.06–1.64) | 1.30 × 10−2 | 3.36 × 10−2 | 0.989 | |
| rs7749730 | G/A | 0.17 | 0.15 | 0.15 | 0.17 | 1.06 (0.89–1.26) | 5.14 × 10−1 | 5.56 × 10−1 | 0.387 | |
| rs12682266 | A/G | 0.50 | 0.50 | 0.47 | 0.46 | 1.01 (0.89–1.14) | 8.97 × 10−1 | 6.86 × 10−1 | 1.000 | |
| rs12100561 | A/G | 0.41 | 0.40 | 0.39 | 0.41 | 1.00 (0.88–1.14) | 9.42 × 10−1 | 6.96 × 10−1 | 0.952 | |
| rs455804 | A/C | 0.33 | 0.32 | 0.29 | 0.32 | 1.00 (0.87–1.15) | 9.88 × 10−1 | 7.06 × 10−1 | 0.831 | |
RAF, risk allele frequency; OR, odds ratio; CI, confidence interval.
aMinor allele/major allele.
bRAF means the allele frequency of cases is lower than that of controls in the Shanghai cohort or both of the two cohorts.
cThe data was analyzed by meta-analysis using the fixed-effects model (the Mantel-Haenszel model) based on the association results, which were generated by logistic regression analysis under an additive model adjusting for gender and age in the two cohorts.
dThe ORs and 95%CIs were calculated by considering the non-risk allele as a reference.
eFalse discovery rate (FDR) correction for multiple testing.
Results of association between SNPs previously reported by HCV-related HCC GWAS and the risk of progression from CHB to LC.
| Gene | SNP | Allele | RAF | RAF | ORmeta (95%CI) | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Cases | Controls | Cases | Controls | |||||||
| rs2596542 | T/C | 0.30 | 0.28 | 0.29 | 0.25 | 1.10 (0.96–1.26) | 1.65 × 10−1 | 2.87 × 10−1 | 0.999 | |
| rs9275572 | A/G | 0.24 | 0.24 | 0.26 | 0.24 | 1.04 (0.90–1.20) | 6.14 × 10−1 | 5.99 × 10−1 | 0.998 | |
| rs1012068 | G/T | 0.25 | 0.24 | 0.24 | 0.24 | 0.99 (0.85–1.14) | 8.64 × 10−1 | 6.78 × 10−1 | 0.945 | |
RAF, risk allele frequency; OR, odds ratio; CI, confidence interval.
aMinor allele/major allele.
bRAF means the allele frequency of cases is lower than that of controls in the Shanghai cohort or both of the two cohorts.
cThe data was analyzed by meta-analysis using the fixed-effects model (the Mantel-Haenszel model) based on the association results, which were generated by logistic regression analysis under an additive model adjusting for gender and age in the two cohorts.
dThe ORs and 95%CIs were calculated by considering the non-risk allele as a reference.
eFalse discovery rate (FDR) correction for multiple testing.
Figure 1Plot of the increasing crude ORs for hepatitis B virus-related liver cirrhosis with increasing number of risk alleles.
The vertical bars represent the 95% confidence intervals.