title: Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level.
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.
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA; National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
authors.forename: Da Wei
authors.initials: DW
authors.lastname: Huang
authors.affiliation: Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Castle
authors.initials: C
authors.lastname: Raley
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Min Kang
authors.initials: MK
authors.lastname: Jiang
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Dun
authors.initials: D
authors.lastname: Liang
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: M Tauseef
authors.initials: MT
authors.lastname: Rehman
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Helene C
authors.initials: HC
authors.lastname: Highbarger
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Jiao
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Brad
authors.initials: B
authors.lastname: Sherman
authors.affiliation: Critical Care Medicine Department, National Institutes of Health, Bethesda, MD, 20892, USA.
authors.forename: Liang
authors.initials: L
authors.lastname: Ma
authors.affiliation: Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Chen
authors.affiliation: Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Skelly
authors.affiliation: Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA; National Human Genome Research Institute, National Institutes of Health, Rockville, MD, 20852, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Troyer
authors.affiliation: Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Stephens
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Tomozumi
authors.initials: T
authors.lastname: Imamichi
authors.affiliation: Division of Clinical Research, National Institute of Allergy & Infectious Diseases, USA.
authors.forename: Alice
authors.initials: A
authors.lastname: Pau
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Lempicki
authors.affiliation: Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Bao
authors.initials: B
authors.lastname: Tran
authors.affiliation: Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Dwight
authors.initials: D
authors.lastname: Nissley
authors.affiliation: Division of Clinical Research, National Institute of Allergy & Infectious Diseases, USA.
authors.forename: H Clifford
authors.initials: HC
authors.lastname: Lane
authors.affiliation: Applied and Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, MD 21702, USA.
authors.forename: Robin L
authors.initials: RL
authors.lastname: Dewar
keywords: HIV-1 drug resistance mutation; Haplotype; Linkage; Next generation sequencing; PacBio; Quasispecies; Single nucleotide variant; Tag-sequence; Third generation sequencing