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Author Notes:

To whom correspondence should be addressed: Eric Hunter. Tel: +1 404 727 8587; Fax: +1 404 727 9316; Email: ehunte4@emory.edu

Conflict of interest statement. M.B. and E.P. are employees of Pacific Biosciences Inc.

Subjects:

Research Funding:

amfAR [Mathilde Krim Fellowship in Basic Biomedical Research; 108672-5-RKGN to D.D.]; Institute of Allergy and Infectious Diseases at the National Institutes of Health [R01 AI64060 and R37 AI51231 to E.H.]; Virology Core at the Emory Center for AIDS Research [P30 AI050409] (in part); Yerkes National Primate Research Center base grant [2P51RR000165-51] through the National Center for Research Resources [P51RR165]; Office of Research Infrastructure Programs/OD [P51OD11132]; Action Cycling Fellowships (to D. D., D. M. and M. D.); E.H. is a Georgia Eminent Scholar.

Funding for open access charge: Institute of Allergy and Infectious Diseases at the National Institutes of Health [R01 AI64060 and R37 AI51231 to E.H.]; amfAR [108672-55-RKGN to D.D.].

Keywords:

  • Science & Technology
  • Life Sciences & Biomedicine
  • Biochemistry & Molecular Biology
  • IMMUNODEFICIENCY-VIRUS TYPE-1
  • DRUG-RESISTANCE
  • HETEROSEXUAL TRANSMISSION
  • DISCORDANT COUPLES
  • RATES
  • AMPLIFICATION
  • MUTATIONS
  • EVOLUTION
  • INFECTION
  • THERAPY

Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing

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Journal Title:

Nucleic Acids Research

Volume:

Volume 43, Number 20

Publisher:

, Pages e129-e129

Type of Work:

Article | Final Publisher PDF

Abstract:

Single Molecule, Real-Time (SMRT®) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.

Copyright information:

© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).

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