ArticleJournal of data mining in genomics & proteomics2016
Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.
Article in Journal of data mining in genomics & proteomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 29 citations in OpenAlex.
- QoALa: A comprehensive workflow for viral quasispecies diversity comparison using long-read sequencing data.PLoS computational biology · 2026Article
- CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads.Bioinformatics (Oxford, England) · 2022Article
- Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology.Applied and environmental microbiology · 2021Review
- MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.Nucleic acids research · 2021Article
- Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections.Frontiers in microbiology · 2021Review
- Short Communication: HIV-DRLink: A Tool for Reporting Linked HIV-1 Drug Resistance Mutations in Large Single-Genome Data Sets Using the Stanford HIV Database.AIDS research and human retroviruses · 2020Article
- Exploring the hepatitis C virus genome using single molecule real-time sequencing.World journal of gastroenterology · 2019Review
- The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach.Frontiers in microbiology · 2019Review
- Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.PLoS computational biology · 2018Article
- Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection.Viruses · 2018Article
- Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues.Journal of neurovirology · 2018Article
- Towards Personalized Medicine: An ImprovedBioinformation · 2018Article
- Article
- A comparative study on the characterization of hepatitis B virus quasispecies by clone-based sequencing and third-generation sequencing.Emerging microbes & infections · 2017Article
- Copy-number variation is an important contributor to the genetic causality of inherited retinal degenerations.Genetics in medicine : official journal of the American College of Medical Genetics · 2017Article
- Evolution of multi-drug resistant HCV clones from pre-existing resistant-associated variants during direct-acting antiviral therapy determined by third-generation sequencing.Scientific reports · 2017Article
- Next-Generation Sequencing: a Diagnostic One-Stop Shop for Hepatitis C?Journal of clinical microbiology · 2016Article
Corrections and comments
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Authors and funding
21 authors at 1 institution in 1 country.
Funding
Abstract
Development of HIV-1 drug resistance mutations (HDRMs) is one of the major reasons for the clinical failure of antiretroviral therapy. Treatment success rates can be improved by applying personalized anti-HIV regimens based on a patient's HDRM profile. However, the sensitivity and specificity of the HDRM profile is limited by the methods used for detection. Sanger-based sequencing technology has traditionally been used for determining HDRM profiles at the single nucleotide variant (SNV) level, but with a sensitivity of only ≥ 20% in the HIV population of a patient. Next Generation Sequencing (NGS) technologies offer greater detection sensitivity (~ 1%) and larger scope (hundreds of samples per run). However, NGS technologies produce reads that are too short to enable the detection of the physical linkages of individual SNVs across the haplotype of each HIV strain present. In this article, we demonstrate that the single-molecule long reads generated using the Third Generation Sequencer (TGS), PacBio RS II, along with the appropriate bioinformatics analysis method, can resolve the HDRM profile at a more advanced quasispecies level. The case studies on patients' HIV samples showed that the quasispecies view produced using the PacBio method offered greater detection sensitivity and was more comprehensive for understanding HDRM situations, which is complement to both Sanger and NGS technologies. In conclusion, the PacBio method, providing a promising new quasispecies level of HDRM profiling, may effect an important change in the field of HIV drug resistance research.
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