PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads.
BLV
Clonal expansion
HIV
HPV
HTLV-1
Integration site analysis
Long-read sequencing
NGS
Retrovirus
Viral genome
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
06 04 2021
06 04 2021
Historique:
received:
18
09
2020
accepted:
25
02
2021
entrez:
7
4
2021
pubmed:
8
4
2021
medline:
12
1
2022
Statut:
epublish
Résumé
The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
Identifiants
pubmed: 33823910
doi: 10.1186/s13059-021-02307-0
pii: 10.1186/s13059-021-02307-0
pmc: PMC8025556
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
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