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“Deep” Sequencing Accuracy and Reproducibility Using Roche/454 Technology for Inferring Co-Receptor Usage in HIV-1

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Listed:
  • David J H F Knapp
  • Rachel A McGovern
  • Art F Y Poon
  • Xiaoyin Zhong
  • Dennison Chan
  • Luke C Swenson
  • Winnie Dong
  • P Richard Harrigan

Abstract

Next generation, “deep”, sequencing has increasing applications both clinically and in disparate fields of research. This study investigates the accuracy and reproducibility of “deep” sequencing as applied to co-receptor prediction using the V3 loop of Human Immunodeficiency Virus-1. Despite increasing use in HIV co-receptor prediction, the accuracy and reproducibility of deep sequencing technology, and the factors which can affect it, have received only a limited level of investigation. To accomplish this, repeated deep sequencing results were generated using the Roche GS-FLX (454) from a number of sources including a non-homogeneous clinical sample (N = 47 replicates over 18 deep sequencing runs), and a large clinical cohort from the MOTIVATE and A400129 studies (N = 1521). For repeated measurements of a non-homogeneous clinical sample, increasing input copy number both decreased variance in the measured proportion of non-R5 using virus (p

Suggested Citation

  • David J H F Knapp & Rachel A McGovern & Art F Y Poon & Xiaoyin Zhong & Dennison Chan & Luke C Swenson & Winnie Dong & P Richard Harrigan, 2014. "“Deep” Sequencing Accuracy and Reproducibility Using Roche/454 Technology for Inferring Co-Receptor Usage in HIV-1," PLOS ONE, Public Library of Science, vol. 9(6), pages 1-10, June.
    • Handle: RePEc:plo:pone00:0099508
    DOI: 10.1371/journal.pone.0099508
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    1. Marcel Margulies & Michael Egholm & William E. Altman & Said Attiya & Joel S. Bader & Lisa A. Bemben & Jan Berka & Michael S. Braverman & Yi-Ju Chen & Zhoutao Chen & Scott B. Dewell & Lei Du & Joseph , 2005. "Genome sequencing in microfabricated high-density picolitre reactors," Nature, Nature, vol. 437(7057), pages 376-380, September.
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