viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome.
Stud Health Technol Inform
; 294: 834-838, 2022 May 25.
Article
em En
| MEDLINE
| ID: mdl-35612221
ABSTRACT
INTRODUCTION:
The implication of viruses in human cancers, as well as the emergence of next generation sequencing has permitted to investigate further their role and pathophysiology in the development of this disease. One such mechanism is the integration of portions of viral genomes in the human genome, as well as the specific action of viral oncogenes.inding integration sites and preserved oncogenes is still relying on heavy manual intervention.METHODS:
We developed an analysis and interpretation pipeline to determine viral insertions. Using data from directed viral capture, the pipeline conducts a crude genotyping phase to select reference viral genomes, identifies chimeric reads, extracts the putative human sequences to locate in the human reference genome, scores and ranks candidate junctions, and exports tabular and visual results.RESULTS:
We leverage common bioinformatics tools (bowtie2, samtools, blat), and a dedicated filtering and ranking algorithm, implemented in R, to infer candidate junctions and insertions. Static results (tables, figures) are produced, as well as an interactive interpretation tool developed as a shiny web app.DISCUSSION:
We validated this pipeline against published results of HPV, HBV, and AAV2 insertions and show good information retrieval.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Vírus
/
Biologia Computacional
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Stud Health Technol Inform
Assunto da revista:
INFORMATICA MEDICA
/
PESQUISA EM SERVICOS DE SAUDE
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
França