Improved Detection of Rare HIV-1 Variants using 454 Pyrosequencing

Quality Score Based Identification and Correction of Pyrosequencing Errors

(2013) Shyamala Iyer et al.   PLoS One

Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications

(2012) Ina Vandenbroucke et al.   BIOTECHNIQUES

Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes

(2012) E. A. Becker et al.   Genome Biology and Evolution

Virologic Failures on Initial Boosted-PI Regimen Infrequently Possess Low-Level Variants with Major PI Resistance Mutations by Ultra-Deep Sequencing

(2012) Max Lataillade et al.   PLoS One

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

(2012) Alexander R. Macalalad et al.   PLoS Computational Biology

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data

(2011) Mattia C. F. Prosperi et al.   BIOINFORMATICS

Inferring viral quasispecies spectra from 454 pyrosequencing reads

(2011) Irina Astrovskaya et al.   BMC BIOINFORMATICS

pcrEfficiency: a Web tool for PCR amplification efficiency prediction

(2011) Izaskun Mallona et al.   BMC BIOINFORMATICS

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

(2011) André Gilles et al.   BMC GENOMICS

Identification of HIV Superinfection in Seroconcordant Couples in Rakai, Uganda, by Use of Next-Generation Deep Sequencing

(2011) A. D. Redd et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

(2011) S. Gianella et al.   JOURNAL OF VIROLOGY

Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial

(2011) Morgane Rolland et al.   NATURE MEDICINE

Viral Linkage in HIV-1 Seroconverters and Their Partners in an HIV-1 Prevention Clinical Trial

(2011) Mary S. Campbell et al.   PLoS One

Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing

(2011) Ellen Knierim et al.   PLoS One

Prevalence and Impact of Minority Variant Drug Resistance Mutations in Primary HIV-1 Infection

(2011) Joanne D. Stekler et al.   PLoS One

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep Molecular Characterization of HIV-1 Dynamics under Suppressive HAART

(2011) Maria J. Buzón et al.   PLoS Pathogens

Transmission of HIV‐1 Drug‐Resistant Variants: Prevalence and Effect on Treatment Outcome

(2010) Martin R. Jakobsen et al.   CLINICAL INFECTIOUS DISEASES

Efficient Suppression of Minority Drug‐Resistant HIV Type 1 (HIV‐1) Variants Present at Primary HIV‐1 Infection by Ritonavir‐Boosted Protease Inhibitor–Containing Antiretroviral Therapy

(2010) Karin J. Metzner et al.   JOURNAL OF INFECTIOUS DISEASES

Whole-Genome Characterization of Human and Simian Immunodeficiency Virus Intrahost Diversity by Ultradeep Pyrosequencing

(2010) B. N. Bimber et al.   JOURNAL OF VIROLOGY

Mathematical Modeling of Ultradeep Sequencing Data Reveals that Acute CD8+ T-Lymphocyte Responses Exert Strong Selective Pressure in Simian Immunodeficiency Virus-Infected Macaques but Still Fail To Clear Founder Epitope Sequences

(2010) T. M. T. Love et al.   JOURNAL OF VIROLOGY

Nucleic Acid Template and the Risk of a PCR-Induced HIV-1 Drug Resistance Mutation

(2010) Vici Varghese et al.   PLoS One

Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing

(2010) Charlotte Hedskog et al.   PLoS One

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

Transmission of HIV-1 minority-resistant variants and response to first-line antiretroviral therapy

(2009) Olivia Peuchant et al.   AIDS

Low-Frequency K103N Strengthens the Impact of Transmitted Drug Resistance on Virologic Responses to First-Line Efavirenz or Nevirapine-Based Highly Active Antiretroviral Therapy

(2009) Anna Maria Geretti et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naïve patients and their impact on the virological failure

(2009) Melanie Balduin et al.   JOURNAL OF CLINICAL VIROLOGY

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

Ultradeep Pyrosequencing Detects Complex Patterns of CD8+ T-Lymphocyte Escape in Simian Immunodeficiency Virus-Infected Macaques

(2009) B. N. Bimber et al.   JOURNAL OF VIROLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Minority Quasispecies of Drug‐Resistant HIV‐1 That Lead to Early Therapy Failure in Treatment‐Naive and ‐Adherent Patients

(2008) Karin J. Metzner et al.   CLINICAL INFECTIOUS DISEASES

Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial

(2008) Susan P Buchbinder et al.   LANCET

Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment–Naïve Populations and Associate with Reduced Treatment Efficacy

(2008) Jeffrey A Johnson et al.   PLOS MEDICINE