ViroISDC:一种基于特征编码的方法来调用乙型肝炎病毒的集成部位
Lei Qiao1, Chang Li1, Wei Lin2
1College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
BMC bioinformatics
|May 4, 2024
概括
一种新的深度学习方法ViroISDC准确地检测人类基因组中的乙型肝炎病毒 (HBV) 整合点. 这一进展提高了对与HBV相关的基因组不稳定性和肝癌发展的理解.
科学领域:
- 基因组学就是基因组学.
- 病毒学 病毒学
- 生物信息学是一种生物信息学.
背景情况:
- 乙型肝炎病毒 (HBV) 整合到人类染色体中可以导致基因组不稳定性和肝癌 (肝癌发生).
- 现有的检测HBV融合地点的方法缺乏精度和稳定性.
研究的目的:
- 开发和验证一种基于深度学习的新方法ViroISDC,用于准确检测HBV集成站点.
- 分析HBV整合模式及其与肝癌发生的关联.
主要方法:
- 维罗ISDC利用深度学习,生成语法规则和编码语言数据特征,用于集成站点预测.
- 性能与已知工具如Lumpy,Pindel,Seeksv和SurVirus进行了比较.
主要成果:
- 与现有方法相比,ViroISDC表现出卓越的性能,可靠性,稳定性和通用性.
- 它对测序深度和集成序列长度不那么敏感.
- 分析揭示了染色体对HBV整合的偏好,倾向于整合到癌细胞组织中,在男性中更高的频率,以及与癌症相关基因的关联.
结论:
- 维罗ISDC管道为HBV集成部位检测提供了更高的精度和可靠性.
- 它为HBV感染提供了宝贵的见解,有助于肝细胞癌 (HCC) 的诊断,治疗和预后.
相关概念视频
Viral Recombination
22.3K
Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
22.3K
Retroviruses
12.1K
Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
12.1K
Size and Structure of Viral Genomes
1.2K
Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
1.2K
Viruses with RNA Genomes
1.5K
RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
1.5K
Hepatitis
86
Hepatitis is an inflammatory condition of the liver most commonly caused by hepatotropic viruses (A–E), though non-infectious causes such as alcohol and drugs also exist.Hepatitis AHepatitis A virus (HAV) is a non-enveloped RNA virus of the Picornaviridae family. It is primarily transmitted via the fecal-oral route, typically through ingestion of contaminated food or water. After ingestion, HAV enters the bloodstream through the oropharynx or intestinal epithelium and reaches the liver.
86
Viral Hepatitis I: Introduction
25
Viral hepatitis is an inflammatory condition of the liver caused by infection with hepatotropic viruses, most commonly hepatitis A, B, C, D, and E. Despite variations in structure and transmission, all viruses mentioned infect hepatocytes and provoke immune responses that can hinder liver function. Additionally, some non-hepatotropic viruses can also lead to hepatic inflammation.Hepatitis A VirusHepatitis A virus (HAV) is transmitted through the fecal–oral route, typically by ingestion...
25


