title: Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes.
abstract: BACKGROUND
  To identify the determinants of successful antiretroviral (ARV) therapy, researchers study the virological responses to treatment-change episodes (TCEs) accompanied by baseline plasma HIV-1 RNA levels, CD4+ T lymphocyte counts, and genotypic resistance data. Such studies, however, often differ in their inclusion and virological response criteria making direct comparisons of study results problematic. Moreover, the absence of a standard method for representing the data comprising a TCE makes it difficult to apply uniform criteria in the analysis of published studies of TCEs.
  
  
  RESULTS
  To facilitate data sharing for TCE analyses, we developed an XML (Extensible Markup Language) Schema that represents the temporal relationship between plasma HIV-1 RNA levels, CD4 counts and genotypic drug resistance data surrounding an ARV treatment change. To demonstrate the adaptability of the TCE XML Schema to different clinical environments, we collaborate with four clinics to create a public repository of about 1,500 TCEs. Despite the nascent state of this TCE XML Repository, we were able to perform an analysis that generated a novel hypothesis pertaining to the optimal use of second-line therapies in resource-limited settings. We also developed an online program (TCE Finder) for searching the TCE XML Repository and another program (TCE Viewer) for generating a graphical depiction of a TCE from a TCE XML Schema document.
  
  
  CONCLUSIONS
  The TCE Suite of applications - the XML Schema, Viewer, Finder, and Repository - addresses several major needs in the analysis of the predictors of virological response to ARV therapy. The TCE XML Schema and Viewer facilitate sharing data comprising a TCE. The TCE Repository, the only publicly available collection of TCEs, and the TCE Finder can be used for testing the predictive value of genotypic resistance interpretation systems and potentially for generating and testing novel hypotheses pertaining to the optimal use of salvage ARV therapy.
authors.affiliation: Department of Medicine, Stanford University, Stanford, CA, USA. syrhee@stanford.edu.
authors.forename: Soo-Yon
authors.initials: SY
authors.lastname: Rhee
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Blanco
authors.forename: Tommy F
authors.initials: TF
authors.lastname: Liu
authors.forename: Iñaki
authors.initials: I
authors.lastname: Pere
authors.forename: Rolf
authors.initials: R
authors.lastname: Kaiser
authors.forename: Maurizio
authors.initials: M
authors.lastname: Zazzi
authors.forename: Francesca
authors.initials: F
authors.lastname: Incardona
authors.forename: William
authors.initials: W
authors.lastname: Towner
authors.forename: Josep Maria
authors.initials: JM
authors.lastname: Gatell
authors.forename: Andrea
authors.initials: A
authors.lastname: De Luca
authors.forename: W Jeffrey
authors.initials: WJ
authors.lastname: Fessel
authors.forename: Robert W
authors.initials: RW
authors.lastname: Shafer