title: Quantification of integrated HIV DNA by repetitive-sampling Alu-HIV PCR on the basis of poisson statistics.
abstract: BACKGROUND
  Quantification of integrated proviral HIV DNA by repetitive-sampling Alu-HIV PCR is a candidate virological tool to monitor the HIV reservoir in patients. However, the experimental procedures and data analysis of the assay are complex and hinder its widespread use. Here, we provide an improved and simplified data analysis method by adopting binomial and Poisson statistics.
  
  
  METHODS
  A modified analysis method on the basis of Poisson statistics was used to analyze the binomial data of positive and negative reactions from a 42-replicate Alu-HIV PCR by use of dilutions of an integration standard and on samples of 57 HIV-infected patients. Results were compared with the quantitative output of the previously described Alu-HIV PCR method.
  
  
  RESULTS
  Poisson-based quantification of the Alu-HIV PCR was linearly correlated with the standard dilution series, indicating that absolute quantification with the Poisson method is a valid alternative for data analysis of repetitive-sampling Alu-HIV PCR data. Quantitative outputs of patient samples assessed by the Poisson method correlated with the previously described Alu-HIV PCR analysis, indicating that this method is a valid alternative for quantifying integrated HIV DNA.
  
  
  CONCLUSIONS
  Poisson-based analysis of the Alu-HIV PCR data enables absolute quantification without the need of a standard dilution curve. Implementation of the CI estimation permits improved qualitative analysis of the data and provides a statistical basis for the required minimal number of technical replicates.
authors.affiliation: HIV Translational Research Unit, Department of Internal Medicine, and Ward.DeSpiegelaere@UGent.be.
authors.forename: Ward
authors.initials: W
authors.lastname: De Spiegelaere
authors.affiliation: HIV Translational Research Unit, Department of Internal Medicine, and.
authors.forename: Eva
authors.initials: E
authors.lastname: Malatinkova
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA.
authors.forename: Lindsay
authors.initials: L
authors.lastname: Lynch
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Ghent University, Ghent, Belgium;
authors.forename: Filip
authors.initials: F
authors.lastname: Van Nieuwerburgh
authors.affiliation: HIV Translational Research Unit, Department of Internal Medicine, and.
authors.forename: Peter
authors.initials: P
authors.lastname: Messiaen
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA.
authors.forename: Una
authors.initials: U
authors.lastname: O'Doherty
authors.affiliation: HIV Translational Research Unit, Department of Internal Medicine, and.
authors.forename: Linos
authors.initials: L
authors.lastname: Vandekerckhove
mesh_terms: D020087:Alu Elements / Q000235:genetics*; D004279:DNA, Viral / Q000032:analysis* / Q000235:genetics*; D006678:HIV / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D016012:Poisson Distribution; D016133:Polymerase Chain Reaction
chemical_list: D004279:DNA, Viral