scholarly journals Profile of HBV Integration in the Plasma DNA of Hepatocellular Carcinoma Patients

2019 ◽  
Vol 20 (1) ◽  
pp. 61-68 ◽  
Author(s):  
Weiyang Li ◽  
Xiaofang Cui ◽  
Qing Huo ◽  
Yanwei Qi ◽  
Yuhui Sun ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Next Generation Sequencing ◽  
Hepatitis B ◽  
Direct Evidence ◽  
Plasma Samples ◽  
Plasma Dna ◽  
Initial Experiment ◽  
Integration Sites ◽  
Significant Enrichment ◽  
Generation Sequencing

Background: Hepatitis B Viral (HBV) infection is one of the major causes of Hepatocellular Carcinoma (HCC). Mounting evidence had provided that the HBV integration might be a critical contributor of HCC carcinogenesis. </P><P> Objective and Methods: To explore the profile of HBV integration in the plasma DNA, the method of next-generation sequencing, HBV capture and bioinformatics had been employed to screen for HBV integration sites in the plasma samples. Results: In the initial experiment, a total of 87 breakpoints were detected in the 20 plasma samples. The distribution of breakpoints showed that there was significant enrichment of breakpoints in the region of intron. Furthermore, the HBV breakpoints were prone to occur in the region of X protein (1,700-2,000bp) in the plasma samples. The pathway analysis had revealed that the HBV integrations sites were specifically enriched in the cancer pathway. Conclusion: Altogether, our results had provided direct evidence for the HBV integration in plasma DNA, and they might be potentially useful for future HCC prognosis and diagnosis.

scholarly journals Next-Generation Sequencing-Based Quantitative Detection of Hepatitis B Virus Pre-S Mutants in Plasma Predicts Hepatocellular Carcinoma Recurrence

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 796 ◽  
Author(s):  
Chiao-Fang Teng ◽  
Tsai-Chung Li ◽  
Hsi-Yuan Huang ◽  
Jia-Hui Lin ◽  
Wen-Shu Chen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Next Generation Sequencing ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Gene Segment ◽  
Quantitative Detection ◽  
Next Generation ◽  
B Virus ◽  
Generation Sequencing ◽  
Hcc Recurrence

Hepatocellular carcinoma (HCC) is among the most common and lethal human cancers worldwide. Despite curative resection, high recurrence of HCC remains a big threat, leading to poor patient outcomes. Hepatitis B virus (HBV) pre-S mutants, which harbor deletions over pre-S1 and pre-S2 gene segments of large surface proteins, have been implicated in HCC recurrence. Therefore, a reliable approach for detection of pre-S mutants is urgently needed for predicting HCC recurrence to improve patient survival. In this study, we used a next-generation sequencing (NGS)-based platform for quantitative detection of pre-S mutants in the plasma of HBV-related HCC patients and evaluated their prognostic values in HCC recurrence. We demonstrated that the presence of deletions spanning the pre-S2 gene segment and the high percentage of pre-S2 plus pre-S1 + pre-S2 deletions, either alone or in combination, was significantly and independently associated with poor recurrence-free survival and had greater prognostic performance than other clinicopathological and viral factors in predicting HCC recurrence. Our data suggest that the NGS-based quantitative detection of pre-S mutants in plasma represents a promising approach for identifying patients at high risk for HBV-related HCC recurrence after surgical resection in a noninvasive manner.

scholarly journals Genomic heterogeneity: next-generation sequencing enables biomarker identification for hepatocellular carcinoma

2017 ◽  
Vol 11 (7) ◽  
pp. 515-518 ◽  
Author(s):  
Demosthenes E Ziogas ◽  
Efstathios G Lykoudis ◽  
Dimitrios H Roukos ◽  
Georgios K Glantzounis
Keyword(s):  
Hepatocellular Carcinoma ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Biomarker Identification ◽  
Generation Sequencing

scholarly journals Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma

2018 ◽  
Vol 115 (46) ◽  
pp. E10925-E10933 ◽  
Author(s):  
Peiyong Jiang ◽  
Kun Sun ◽  
Yu K. Tong ◽  
Suk Hang Cheng ◽  
Timothy H. T. Cheng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Peripheral Circulation ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Plasma Samples ◽  
Dna Molecules ◽  
Plasma Dna ◽  
Cell Free Dna ◽  
Free Dna ◽  
Tumor Dna

Circulating tumor-derived cell-free DNA (ctDNA) analysis offers an attractive noninvasive means for detection and monitoring of cancers. Evidence for the presence of cancer is dependent on the ability to detect features in the peripheral circulation that are deemed as cancer-associated. We explored approaches to improve the chance of detecting the presence of cancer based on sequence information present on ctDNA molecules. We developed an approach to detect the total pool of somatic mutations. We then investigated if there existed a class of ctDNA signature in the form of preferred plasma DNA end coordinates. Cell-free DNA fragmentation is a nonrandom process. Using plasma samples obtained from liver transplant recipients, we showed that liver contributed cell-free DNA molecules ended more frequently at certain genomic coordinates than the nonliver-derived molecules. The abundance of plasma DNA molecules with these liver-associated ends correlated with the liver DNA fractions in the plasma samples. Studying the DNA end characteristics in plasma of patients with hepatocellular carcinoma and chronic hepatitis B, we showed that there were millions of tumor-associated plasma DNA end coordinates in the genome. Abundance of plasma DNA molecules with tumor-associated DNA ends correlated with the tumor DNA fractions even in plasma samples of hepatocellular carcinoma patients that were subjected to shallow-depth sequencing analysis. Plasma DNA end coordinates may therefore serve as hallmarks of ctDNA that could be sampled readily and, hence, may improve the cost-effectiveness of liquid biopsy assessment.

Sign in / Sign up

Export Citation Format

Share Document