Related Experiment Video

Updated: Aug 9, 2025

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

17.7K

VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns

Ye Chen1, Yuyan Wang1, Ping Zhou2

  • 1Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China.

Genomics, Proteomics & Bioinformatics
|February 21, 2023
PubMed

Insights

A new Virus Integration Site (VIS) Atlas database catalogs human papillomavirus, hepatitis B virus, and Epstein-Barr virus integration breakpoints. This resource aids research into virus-induced cancers and potential antitumor drug development.

Area of Science:

  • Oncology
  • Virology
  • Bioinformatics

Background:

  • Oncogenic DNA virus integration into the human genome is crucial for viral carcinogenesis.
  • Understanding these integration events is key to deciphering virus-induced cancers.

Purpose of the Study:

  • To create a comprehensive database of virus integration sites (VIS) for major oncoviruses.
  • To provide tools for analyzing integration patterns and genotype-specific features.

Main Methods:

  • Compiled a database of integration breakpoints from next-generation sequencing (NGS) data, literature, and experimental results.
  • Included data for human papillomavirus, hepatitis B virus, and Epstein-Barr virus.
  • Developed a genome browser and statistics interface for data analysis.

Main Results:

  • The VIS Atlas database contains 63,179 breakpoints and 47,411 junctional sequences.
  • Data covers 47 virus genotypes and 17 disease types.
  • The database facilitates breakpoint quality checks and visualization.

Conclusions:

  • The VIS Atlas database offers a valuable resource for studying viral integration patterns.
  • Insights gained can advance understanding of virus pathogenesis and aid in developing new anticancer therapies.
Keywords:
DNA virusIntegration patternNext-generation sequencingVirus genotypeVirus integration site

More Related Videos

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

320
Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow12:53

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Published on: June 14, 2017

10.8K

Related Concept Videos

Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
11.6K
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
47.2K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.4K
DNA-only Transposons02:57

DNA-only Transposons

DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
14.6K