Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

PLoS Comput Biol
Authors
Keywords
Abstract

Viruses diversify over time within hosts, often undercutting the effectiveness of host defenses and therapeutic interventions. To design successful vaccines and therapeutics, it is critical to better understand viral diversification, including comprehensively characterizing the genetic variants in viral intra-host populations and modeling changes from transmission through the course of infection. Massively parallel sequencing technologies can overcome the cost constraints of older sequencing methods and obtain the high sequence coverage needed to detect rare genetic variants ( 97% sensitivity and > 97% specificity on control read sets. On data derived from a patient after four years of HIV-1 infection, V-Phaser detected 2,015 variants across the -10 kb genome, including 603 rare variants (

Year of Publication
2012
Journal
PLoS Comput Biol
Volume
8
Issue
3
Pages
e1002417
Date Published
2012
ISSN
1553-7358
URL
DOI
10.1371/journal.pcbi.1002417
PubMed ID
22438797
PubMed Central ID
PMC3305335
Links
Grant list
P01 AI074415 / AI / NIAID NIH HHS / United States
HHSN272200900006C / AI / NIAID NIH HHS / United States
HHSN272200900006C / PHS HHS / United States
T32 AI007538 / AI / NIAID NIH HHS / United States
HHSN27220090018C / PHS HHS / United States
P01-AI074415 / AI / NIAID NIH HHS / United States