Jia, Jian-An, Zhang, Shuqin, Bai, Xin, Fang, Meng, Chen, Shipeng, Liang, Xiaotao, Zhu, Shanfeng, Wong, Danny Ka-Ho, Zhang, Anye, Feng, Jianfeng, Sun, Fengzhu and Gao, Chunfang (2022) Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma. Virology Journal, 19 (1). 114. doi:10.1186/s12985-022-01836-9 ISSN 1743-422X.
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Abstract
Chronic infection with hepatitis B virus (HBV) has been proved highly associated with the development of hepatocellular carcinoma (HCC). The purpose of the study is to investigate the association between HBV preS region quasispecies and HCC development, as well as to develop HCC diagnosis model using HBV preS region quasispecies. A total of 104 chronic hepatitis B (CHB) patients and 117 HBV-related HCC patients were enrolled. HBV preS region was sequenced using next generation sequencing (NGS) and the nucleotide entropy was calculated for quasispecies evaluation. Sparse logistic regression (SLR) was used to predict HCC development and prediction performances were evaluated using receiver operating characteristic curves. Entropy of HBV preS1, preS2 regions and several nucleotide points showed significant divergence between CHB and HCC patients. Using SLR, the classification of HCC/CHB groups achieved a mean area under the receiver operating characteristic curve (AUC) of 0.883 in the training data and 0.795 in the test data. The prediction model was also validated by a completely independent dataset from Hong Kong. The 10 selected nucleotide positions showed significantly different entropy between CHB and HCC patients. The HBV quasispecies also classified three clinical parameters, including HBeAg, HBVDNA, and Alkaline phosphatase (ALP) with the AUC value greater than 0.6 in the test data. Using NGS and SLR, the association between HBV preS region nucleotide entropy and HCC development was validated in our study and this could promote the understanding of HCC progression mechanism.
| Item Type: | Journal Article |
|---|---|
| Subjects: | Q Science > QA Mathematics Q Science > QR Microbiology R Medicine > RC Internal medicine |
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science |
| SWORD Depositor: | Library Publications Router |
| Library of Congress Subject Headings (LCSH): | Liver -- Cancer, Hepatitis B virus, Species, Logistic regression analysis |
| Journal or Publication Title: | Virology Journal |
| Publisher: | BioMed Central Ltd. |
| ISSN: | 1743-422X |
| Official Date: | 28 June 2022 |
| Dates: | Date Event 28 June 2022 Published 25 May 2022 Accepted |
| Volume: | 19 |
| Number: | 1 |
| Article Number: | 114 |
| DOI: | 10.1186/s12985-022-01836-9 |
| Status: | Peer Reviewed |
| Publication Status: | Published |
| Access rights to Published version: | Open Access (Creative Commons open licence) |
| Date of first compliant deposit: | 25 July 2022 |
| Date of first compliant Open Access: | 26 July 2022 |
| RIOXX Funder/Project Grant: | Project/Grant ID RIOXX Funder Name Funder ID 2019CXJQ03 Shanghai Municipal Health Commission UNSPECIFIED 16JC1402600 Science and Technology Commission of Shanghai Municipality |
| URI: | https://wrap.warwick.ac.uk/167193/ |
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