ArticleScientific reports2015
Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 45 citations in OpenAlex.
- No evidence for active viral infection in unicentric and idiopathic multicentric Castleman disease by Viral-Track analysis.Scientific reports · 2025Article
- Integration of Viral Genome to Human Genomic DNA in Nails of Patients with Chronic Hepatitis B Virus Infection.JMA journal · 2023Article
- VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns.Genomics, proteomics & bioinformatics · 2023Article
- BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations.BMC bioinformatics · 2022Article
- Computational Methods for the Discovery and Annotation of Viral Integrations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Causes and Consequences of HPV Integration in Head and Neck Squamous Cell Carcinomas: State of the Art.Cancers · 2021Review
- SurVirus: a repeat-aware virus integration caller.Nucleic acids research · 2021Article
- Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements.Molecular ecology · 2021Article
- Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection ofViruses · 2021Article
- ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data.BMC bioinformatics · 2021Article
- Improved reference genome of the arboviral vector Aedes albopictus.Genome biology · 2020Article
- VSeq-Toolkit: Comprehensive Computational Analysis of Viral Vectors in Gene Therapy.Molecular therapy. Methods & clinical development · 2020Article
- Review
- A First NGS Investigation Suggests No Association Between Viruses and Canine Cancers.Frontiers in veterinary science · 2020Article
- A virome-wide clonal integration analysis platform for discovering cancer viral etiology.Genome research · 2019Article
- Insights Into an Unexplored Component of the Mosquito Repeatome: Distribution and Variability of Viral Sequences Integrated Into the Genome of the Arboviral VectorFrontiers in genetics · 2019Article
- The precision prevention and therapy of HPV-related cervical cancer: new concepts and clinical implications.Cancer medicine · 2018Review
- ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.Nucleic acids research · 2018Article
- Utility of high-throughput DNA sequencing in the study of the human papillomaviruses.Virus genes · 2018Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several pathogenic viruses such as hepatitis B and human immunodeficiency viruses may integrate into the host genome. These virus/host integrations are detectable using paired-end next generation sequencing. However, the low number of expected true virus integrations may be difficult to distinguish from the noise of many false positive candidates. Here, we propose a novel filtering approach that increases specificity without compromising sensitivity for virus/host chimera detection. Our detection pipeline termed Vy-PER (Virus integration detection bY Paired End Reads) outperforms existing similar tools in speed and accuracy. We analysed whole genome data from childhood acute lymphoblastic leukemia (ALL), which is characterised by genomic rearrangements and usually associated with radiation exposure. This analysis was motivated by the recently reported virus integrations at genomic rearrangement sites and association with chromosomal instability in liver cancer. However, as expected, our analysis of 20 tumour and matched germline genomes from ALL patients finds no significant evidence for integrations by known viruses. Nevertheless, our method eliminates 12,800 false positives per genome (80× coverage) and only our method detects singleton human-phiX174-chimeras caused by optical errors of the Illumina HiSeq platform. This high accuracy is useful for detecting low virus integration levels as well as non-integrated viruses.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.