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Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations

  1. Author:
    Jordan, M. R.
    Kearney, M.
    Palmer, S.
    Shao, W.
    Maldarelli, F.
    Coakley, E. P.
    Chappey, C.
    Wanke, C.
    Coffin, J. M.

  2. Author Address

    [Jordan, Michael R.] Tufts Univ, Div Geog Med & Infect Dis, Tufts Med Ctr, Sch Med, Boston, MA 02111 USA. [Kearney, Mary; Palmer, Sarah; Shao, Wei; Maldarelli, Frank] NCI, HIV Drug Resistance Program, NIH, Frederick, MD 21702 USA. [Palmer, Sarah] Karolinska Inst, Swedish Inst Infect Dis Control, Stockholm, Sweden. [Coakley, Eoin P.] Monogram Biosci Inc, San Francisco, CA 94080 USA. [Chappey, Colombe] Genentech Inc, San Francisco, CA 94080 USA.;Jordan, MR, Tufts Univ, Div Geog Med & Infect Dis, Tufts Med Ctr, Sch Med, 800 Washington St,Box 41,136 Harrison Ave, Boston, MA 02111 USA.;mjordan@tuftsmedicalcenter.org kearneym@ncifcrf.gov sarah.palmer@smi.ki.se shaow@ncifcrf.gov fmalli@mail.nih.gov ecoakley@monogrambio.com colombe.chappey@gmail.com Christine.wanke@tufts.edu john.coffin@tufts.edu
    1. Year: 2010
    2. Date: Sep
  2. Journal: Journal of Virological Methods
    1. 168
    2. 1-2
    3. Pages: 114-120
  4. Type of Article: Article
  5. ISSN: 0166-0934
  1. Abstract:

    To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naive patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity. (C) 2010 Elsevier B.V. All rights reserved.

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External Sources

  1. View Full Text
  2. DOI: 10.1016/j.jviromet.2010.04.030
  3. View record in Web of Science®
  4. WOS: 000280869400020

Library Notes

  1. Fiscal Year: FY2009-2010
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