We have located links that may give you full text access.
Analysis of HBV X Gene Quasispecies Characteristics by Next Generation Sequencing and Cloning-Based Sequencing and Its Association with Hepatocellular Carcinoma Progression.
Journal of Medical Virology 2019 Februrary 4
OBJECTIVES: This study aimed to describe the differences between next-generation sequencing(NGS) and cloning-based sequencing(CBS) in HBX quasispecies research and primitively investigate the relationship between the dominant HBX quasispecies and HCC.
METHODS: A total of 12 serum samples were collected. Serum HBV DNA was extracted and the HBV X region (HBX) was amplified by nested PCR. The PCR products were simultaneously tested with NGS and CBS to detect quasispecies of the HBX.
RESULT: Total 9348 eligible quasispecies sequences were obtained by NGS, which were much larger than the 98 of that by CBS. By the phylogenetic tree, the dominant quasispecies sequence of each sample could be found, although they had several nucleotides differences between the dominant quasispecies sequences found by CBS and NGS. By comparing the quasispecies heterogeneity , it was found that the quasispecies complexity value of HBV X region obtained by NGS was higher than CBS( P<0.05). The diversity values, including d, dS, dN and dN/dS obtained by NGS were lower than by CBS (all of P<0.01). The relativity of Spearman(rs) in d, dS and dN were statistically significant(rs_d=0.865, P=0.001; rs_dS=0.722, P=0.014 and rs_dN=0.738, P=0.011 respectively). There were 21 different bases between the HBX quasispecies of case A and control B.
CONCLUSION: The results of this can be used as guidance when researchers plan to choose a suitable method to study quasispecies, especially the HBV X gene quasispecies. Some high-risk mutations of HBX quasispecies were also found in this study and their relationship with HCC need deeper exploration. This article is protected by copyright. All rights reserved.
METHODS: A total of 12 serum samples were collected. Serum HBV DNA was extracted and the HBV X region (HBX) was amplified by nested PCR. The PCR products were simultaneously tested with NGS and CBS to detect quasispecies of the HBX.
RESULT: Total 9348 eligible quasispecies sequences were obtained by NGS, which were much larger than the 98 of that by CBS. By the phylogenetic tree, the dominant quasispecies sequence of each sample could be found, although they had several nucleotides differences between the dominant quasispecies sequences found by CBS and NGS. By comparing the quasispecies heterogeneity , it was found that the quasispecies complexity value of HBV X region obtained by NGS was higher than CBS( P<0.05). The diversity values, including d, dS, dN and dN/dS obtained by NGS were lower than by CBS (all of P<0.01). The relativity of Spearman(rs) in d, dS and dN were statistically significant(rs_d=0.865, P=0.001; rs_dS=0.722, P=0.014 and rs_dN=0.738, P=0.011 respectively). There were 21 different bases between the HBX quasispecies of case A and control B.
CONCLUSION: The results of this can be used as guidance when researchers plan to choose a suitable method to study quasispecies, especially the HBV X gene quasispecies. Some high-risk mutations of HBX quasispecies were also found in this study and their relationship with HCC need deeper exploration. This article is protected by copyright. All rights reserved.
Full text links
Related Resources
Trending Papers
Heart failure with preserved ejection fraction: diagnosis, risk assessment, and treatment.Clinical Research in Cardiology : Official Journal of the German Cardiac Society 2024 April 12
Proximal versus distal diuretics in congestive heart failure.Nephrology, Dialysis, Transplantation 2024 Februrary 30
Efficacy and safety of pharmacotherapy in chronic insomnia: A review of clinical guidelines and case reports.Mental Health Clinician 2023 October
World Health Organization and International Consensus Classification of eosinophilic disorders: 2024 update on diagnosis, risk stratification, and management.American Journal of Hematology 2024 March 30
Get seemless 1-tap access through your institution/university
For the best experience, use the Read mobile app
All material on this website is protected by copyright, Copyright © 1994-2024 by WebMD LLC.
This website also contains material copyrighted by 3rd parties.
By using this service, you agree to our terms of use and privacy policy.
Your Privacy Choices
You can now claim free CME credits for this literature searchClaim now
Get seemless 1-tap access through your institution/university
For the best experience, use the Read mobile app