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Rhee SY, Blanco JL, Liu TF, Pere I, Kaiser R, Zazzi M, Incardona F, Towner W, Gatell JM, De Luca A, Fessel WJ, Shafer RW. Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes. AIDS Res Ther 2012; 9:13. [PMID: 22554313 PMCID: PMC3439255 DOI: 10.1186/1742-6405-9-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 03/16/2012] [Indexed: 11/23/2022] Open
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.
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Affiliation(s)
- Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, CA, USA
- Division of Infectious Diseases, Room S-169, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Jose Luis Blanco
- Hospital Clinic Universitari-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Tommy F Liu
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Iñaki Pere
- Hospital Clinic Universitari-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Rolf Kaiser
- Institute of Virology, EuResist Network GEIE, University of Cologne, Cologne, Germany
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, EuResist Network GEIE, University of Siena, Siena, Italy
| | | | - William Towner
- Department of Infectious Disease, Kaiser Permanente, Los Angeles, CA, USA
| | - Josep Maria Gatell
- Hospital Clinic Universitari-IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Andrea De Luca
- Institute of Clinical Infectious Diseases, Catholic University of Sacred Heart, Rome, Italy
- Unit of Infectious Diseases 2, University Hospital of Siena, Siena, Italy
| | - W Jeffrey Fessel
- Kaiser Permanente Medical Care Program, South San Francisco, CA, USA
| | - Robert W Shafer
- Department of Medicine, Stanford University, Stanford, CA, USA
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