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Standardized Representation, Visualization and Searchable Rhee et al. AIDS Research and Therapy 2012, 9:13 http://www.aidsrestherapy.com/content/9/1/13 METHODOLOGY Open Access Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes Soo-Yon Rhee1,10*, Jose Luis Blanco2, Tommy F Liu1, Iñaki Pere2, Rolf Kaiser3, Maurizio Zazzi4, Francesca Incardona5, William Towner6, Josep Maria Gatell2, Andrea De Luca7,8, W Jeffrey Fessel9 and Robert W Shafer1 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. Keywords: Human immunodeficiency virus, Antiretroviral treatment, Drug resistance, Clinical outcomes, XML schema, Database Background resistance genotype results, and the subsequent virological To identify determinants of successful antiretroviral (ARV) response to a salvage therapy regimen [2-8]. Such studies, therapy in HIV-1-infected patients for whom a previous however, often differ in their inclusion criteria, salvage ther- ARV treatment regimen has failed, researchers study clin- apy requirements, and definition of virological response. ical data associated with treatment-change episodes (TCEs) To facilitate data sharing and analyses of combined [1]. These studies characterize the relationship between past data, we have developed a TCE XML Schema to repre- ARV treatments, plasma HIV-1 RNA levels, HIV-1 drug sent treatment-change episodes. XML (Extensible Markup Language) is a markup language for encoding * Correspondence: [email protected] human and computer readable documents. An XML 1Department of Medicine, Stanford University, Stanford, CA, USA Schema defines constrained elements and attributes that 10Division of Infectious Diseases, Room S-169, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA 94305, USA can ensure a consistent representation of complex data. Full list of author information is available at the end of the article The TCE XML Schema is a richer representation of data © 2012 Rhee et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Rhee et al. AIDS Research and Therapy 2012, 9:13 Page 2 of 8 http://www.aidsrestherapy.com/content/9/1/13 than the flat files or spreadsheets, which form the basis The TCE Viewer accepts an XML file, validates the file for most analyses [9]. Here we collaborate with four clinics against the TCE Schema, and generates a graphical de- to create a public repository of 1,500 TCE XML documents piction of the TCE containing three sections: (i) a figure represented using the TCE XML Schema (TCE Repository). with the ARV regimens, plasma HIV-1 RNA levels, and To demonstrate the utility of such a repository for hypoth- CD4 counts preceding and following the treatment esis generation and knowledge discovery, we analyzed a sub- change; (ii) a table with one or more genotypic resistance set of the repository to obtain insights into the optimal use test results preceding the treatment change; and (iii) a of second-line therapy in resource-limited settings. compressed summary of the virological and immuno- We also describe two online programs that complement logical responses to past ARV regimens. The TCE the TCE XML Schema: a TCE Viewer and a TCE Finder. Viewer provides an additional mechanism of validation The TCE Viewer accepts a valid TCE XML Schema docu- because many clinicians are adept at visually recognizing ment and creates a graphical depiction of the temporal re- anomalous clinical patterns that may have resulted from lationship between ARV regimens, plasma HIV-1 RNA data entry errors. levels, peripheral blood CD4+ T lymphocyte counts (CD4 counts), and genotypic resistance data. The TCE Finder TCE finder searches the TCE Repository according to user-defined cri- The TCE Finder enables users to identify TCEs meeting teria and retrieves those that meet the search criteria. user-defined search criteria (http://hivdb.stanford.edu/ TCEs/cgi-bin/TCE_finder.cgi). The TCE Finder accepts in- Methods put parameters pertaining to the ARVs used prior to the TCE XML schema change in therapy and/or to the ARVs used for salvage The TCE XML Schema elements and constraints were therapy. A summary of the TCEs matching the input cri- developed to represent the temporal relationship among teria are then presented to the user in a table that contains ARVs, plasma HIV-1 RNA levels, CD4 counts and geno- the following fields: ARVs received and genotypic resistance typic drug resistance data surrounding a treatment test results obtained prior to baseline, the salvage ARV regi- change. Each valid TCE XML Schema document must men, and plasma HIV-1 RNA levels obtained while taking have a treatment change time point (baseline or time the salvage ARV regimen. The table also contains a thumb- zero). The TCE baseline must be assigned a date or, at nail image of each TCE that links to the graphical depiction the very minimum, a calendar year. The preceding and of the TCE created by the TCE Viewer. subsequent data are demarcated by the number of weeks from baseline. The complete treatment history received Results before baseline is represented as a list of regimens, their TCE repository durations, and associated plasma HIV-1 RNA levels and To demonstrate the ability of the TCE Schema to represent CD4 counts. However, if these data are not available, the data from different clinics, we collaborated with four clinics XML Schema can represent the past treatment history as to create a publicly available TCE repository. For the pur- a list of one or more ARVs or ARV classes. Genotypic poses of our collaboration we selected TCEs sharing each drug resistance test results are represented as nucleotide of the following criteria: (i) evidence for virological failure sequences or lists of amino acid mutations obtained prior to a change in therapy defined a plasma HIV-1 RNA prior to the treatment change. Optional elements include level of >1,000 copies/ml obtained within 8 weeks before the nadir CD4 count, gender, age, ethnicity, and a meta- the change; (ii) a complete list of ARVs received prior to data element for either annotating or just naming the baseline; (iii) a change in ARVs occurring within 24 weeks TCE. The TCE XML Schema can be found at http:// of a baseline genotypic resistance test; (iv) a new salvage hivdb.stanford.edu/TCEs/schema/TCE.xsd. regimen administered for at least four weeks; (v) one or To demonstrate the adaptability of the TCE XML more CD4 counts within 24 weeks prior to the ARV Schema to different clinical environments, we collabo- change; and (vi) two or more plasma HIV-1 RNA levels rated with four clinics from Kaiser-Permanente Medical within the first 36 weeks while taking the salvage regimen. Care Program-Northern/Southern California, University Overall, 1,527 TCEs met the above inclusion criteria in- of Barcelona and EuResist Network Database. The study cluding 1,217 from Northern California, 162 from the Uni- was approved by the Stanford University Institutional versity of Barcelona, 90 from Southern California and 58 Review Board (“Clinical Significance of HIV-1 Drug Re- from the EuResist Network Database. The TCEs occurred sistance: A Clinic Based Approach”, Protocol ID: 13900). between 1998 and 2010: 555 between 1998 and 2000; 550 between 2001 and 2003; 228 between 2004 and 2006; 195 TCE viewer between 2007 and 2010. The median CD4 nadir was 108 The TCE Viewer creates a graphical depiction of a TCE (IQR:34to213).ThemedianplasmaHIV-1RNAlevels (http://hivdb.stanford.edu/TCEs/cgi-bin/TCE_viewer.cgi). and CD4 counts were 4.2 log copies/ml (IQR: 3.7 to 4.7) Rhee et al. AIDS Research and Therapy 2012, 9:13 Page 3 of 8 http://www.aidsrestherapy.com/content/9/1/13 and 257 (IQR: 139 to 402), respectively. Patients had Table 2 Summary of the ARV Class Combinations received a median six years (IQR: 3 to 8) of ARV therapy Comprising the Salvage ARV Regimens prior to the TCE.
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