Abstract:
BACKGROUND:Next-generation sequencing (NGS) is a powerful and high-throughput method for the detection of viral mutations. This article provides a brief overview about optimization of NGS analysis for hepatocellular carcinoma (HCC)-associated hepatitis B virus (HBV) mutations, and hepatocarcinogenesis of relevant mutations. MAIN BODY:For the application of NGS analysis in the genome of HBV, four noteworthy steps were discovered in testing. First, a sample-specific reference sequence was the most effective mapping reference for NGS. Second, elongating the end of reference sequence improved mapping performance at the end of the genome. Third, resetting the origin of mapping reference sequence could probed deletion mutations and variants at a certain location with common mutations. Fourth, using a platform-specific cut-off value to distinguish authentic minority variants from technical artifacts was found to be highly effective. One hundred and sixty-seven HBV single nucleotide variants (SNVs) were found to be studied previously through a systematic literature review, and 12 SNVs were determined to be associated with HCC by meta-analysis. From comprehensive research using a HBV genome-wide NGS analysis, 60 NGS-defined HCC-associated SNVs with their pathogenic frequencies were identified, with 19 reported previously. All the 12 HCC-associated SNVs proved by meta-analysis were confirmed by NGS analysis, except for C1766T and T1768A which were mainly expressed in genotypes A and D, but including the subgroup analysis of A1762T. In the 41 novel NGS-defined HCC-associated SNVs, 31.7% (13/41) had cut-off values of SNV frequency lower than 20%. This showed that NGS could be used to detect HCC-associated SNVs with low SNV frequency. Most SNV II (the minor strains in the majority of non-HCC patients) had either low (< 20%) or high (> 80%) SNV frequencies in HCC patients, a characteristic U-shaped distribution pattern. The cut-off values of SNV frequency for HCC-associated SNVs represent their pathogenic frequencies. The pathogenic frequencies of HCC-associated SNV II also showed a U-shaped distribution. Hepatocarcinogenesis induced by HBV mutated proteins through cellular pathways was reviewed. CONCLUSION:NGS analysis is useful to discover novel HCC-associated HBV SNVs, especially those with low SNV frequency. The hepatocarcinogenetic mechanisms of novel HCC-associated HBV SNVs defined by NGS analysis deserve further investigation.
journal_name
J Biomed Scijournal_title
Journal of biomedical scienceauthors
Wu IC,Liu WC,Chang TTdoi
10.1186/s12929-018-0442-4subject
Has Abstractpub_date
2018-06-02 00:00:00pages
51issue
1eissn
1021-7770issn
1423-0127pii
10.1186/s12929-018-0442-4journal_volume
25pub_type
杂志文章,评审abstract::Our goal was to develop a system to study proteins that associate in vivo with the Moloney murine leukemia virus (M-MuLV) enhancer elements by the isolation of intact proviral chromatin. The M-MuLV long terminal repeats (LTRs) contain tandemly repeated transcriptional enhancer sequences consisting of smaller motifs th...
journal_title:Journal of biomedical science
pub_type: 杂志文章
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abstract:BACKGROUND:Promoting post-stroke neurogenesis has long been proposed to be a therapeutic strategy for the enhancement of functional recovery after cerebral ischemic stroke. Despite numerous approaches have been widely reported the proliferation or differentiation of the neurogenic population therapeutic strategies by t...
journal_title:Journal of biomedical science
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journal_title:Journal of biomedical science
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abstract:BACKGROUND:RNA interference (RNAi) is a powerful tool to silence gene expression post-transcriptionally. Delivering sequences of RNAi in vivo remains a problem. The aim of this study was to use JC virus (JCV) virus-like particles (VLPs) as a vector for delivering RNAi in silencing the cytokine gene of IL-10. METHODS:J...
journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/1423-0127-17-51
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abstract::To search for cellular genes up-regulated by vaccinia virus (VV) infection, differential display-reverse transcription-polymerase chain reaction (ddRT-PCR) assays were used to examine the expression of mRNAs from mock-infected and VV-infected HeLa cells. Two mitochondrial genes for proteins that are part of the electr...
journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/1423-0127-16-80
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abstract::A considerable number of animal studies on the effects of dopaminergic agents on alcohol intake behavior have been performed. Acute alcohol administration in rats induces dopamine release in the caudate nucleus and in the nucleus accumbens, an effect related among others to reinforcement. It has been repeatedly sugges...
journal_title:Journal of biomedical science
pub_type: 杂志文章,评审
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1007/BF02253065
更新日期:1995-04-01 00:00:00
abstract:BACKGROUND:To develop an individually-tailored dynamic risk assessment model following a multistep, multifactorial process of the Correa's gastric cancer model. METHODS:First, we estimated the state-to-state transition rates following Correa's five-step carcinogenic model and assessed the effect of risk factors, inclu...
journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/s12929-018-0485-6
更新日期:2018-11-19 00:00:00
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journal_title:Journal of biomedical science
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更新日期:2009-12-09 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/s12929-014-0069-z
更新日期:2014-07-31 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章,评审
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更新日期:2017-09-07 00:00:00
abstract:BACKGROUND:Pneumococcal conjugate vaccine (PCV) reduces both invasive pneumococcal disease (IPD) and other pneumococcal infections worldwide. We investigated the impact of stepwise implementation of childhood PCV programs on the prevalence of pneumococcal pneumonia, severity of acute inflammation, and associations betw...
journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/s12929-020-00680-9
更新日期:2020-08-19 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/1423-0127-20-34
更新日期:2013-05-31 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/1423-0127-19-97
更新日期:2012-11-19 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1007/BF02256059
更新日期:2003-03-01 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/1423-0127-16-85
更新日期:2009-09-21 00:00:00
abstract::Mitochondria are sub-cellular organelles that produce adenosine triphosphate (ATP) through oxidative phosphorylation (OXPHOS). As suggested over 70 years ago by Otto Warburg and recently confirmed with molecular techniques, alterations in respiratory activity and in mitochondrial DNA (mtDNA) appear to be common featur...
journal_title:Journal of biomedical science
pub_type: 杂志文章,评审
doi:10.1186/1423-0127-17-31
更新日期:2010-04-25 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1007/s11373-007-9164-4
更新日期:2007-09-01 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1186/s12929-018-0424-6
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journal_title:Journal of biomedical science
pub_type: 杂志文章,评审
doi:10.1186/1423-0127-16-96
更新日期:2009-10-22 00:00:00
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journal_title:Journal of biomedical science
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doi:10.1186/1423-0127-20-45
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1007/BF02256432
更新日期:2003-07-01 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
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更新日期:2003-11-01 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1007/BF02256094
更新日期:2004-07-01 00:00:00
abstract::Human mesenchymal stem cells (MSCs) are multilineage somatic progenitor/stem cells that have been shown to possess immunomodulatory properties in recent years. Initially met with much skepticism, MSC immunomodulation has now been well reproduced across tissue sources and species to be clinically relevant. This has ope...
journal_title:Journal of biomedical science
pub_type: 杂志文章,评审
doi:10.1186/s12929-016-0289-5
更新日期:2016-11-04 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
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更新日期:2004-09-01 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
doi:10.1007/BF02256440
更新日期:1999-03-01 00:00:00
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journal_title:Journal of biomedical science
pub_type: 杂志文章
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更新日期:2015-04-01 00:00:00
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pub_type: 已发布勘误
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更新日期:2020-09-21 00:00:00
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pub_type: 杂志文章
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