viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome - Archive ouverte HAL
Article Dans Une Revue Studies in Health Technology and Informatics Année : 2022

viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome

Résumé

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.
Fichier principal
Vignette du fichier
SHTI-294-SHTI220602.pdf (370.1 Ko) Télécharger le fichier
Origine Fichiers éditeurs autorisés sur une archive ouverte
Licence

Dates et versions

hal-04147996 , version 1 (01-07-2023)

Licence

Identifiants

Citer

Maxime Wack, David Veyer, Camille Peneau, Sonia Lameiras, William Digan, et al.. viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome. Studies in Health Technology and Informatics, 2022, Studies in Health Technology and Informatics, ⟨10.3233/SHTI220602⟩. ⟨hal-04147996⟩
20 Consultations
31 Téléchargements

Altmetric

Partager

More