Abstract
Despite the availability of antiretroviral combination therapies, success in drug treatment of HIV-infected patients is limited. One reason for therapy failure is the development of drug-resistant genetic variants. In principle, the viral genomic sequence provides resistance information and could thus guide the selection of an optimal drug combination. In practice however, the benefit of this procedure is impaired by (1) the difficulty in inferring the clinically relevant information from the genotype of the virus and (2) the restricted availability of this information. We have developed a secure platform for collaborative research aimed at optimizing anti-HIV therapies, called Arevir. A relational database schema was designed and implemented together with a web-based user interface. Our system provides a basis for monitoring patients, decision-support, and computational analyses. Thus, it merges clinical, diagnostic and bioinformatics efforts to exploit genomic and patient therapy data in clinical practice.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Stanic, A., Schneider, T.K.: Overview of Antiretroviral Agents in 2005. Journal of Pharmacy Practice 18, 228–246 (2005)
Marcello, A.: Latency: the hidden HIV-1 challenge. Retrovirology 3, 7 (2006)
Powderly, W.G.: Long-term exposure to lifelong therapies. J. Acquir. Immune. Defic. Syndr. 29(suppl. 1), S28–S40 (2002)
Perrin, L., Telenti, A.: HIV treatment failure: testing for HIV resistance in clinical practice. Science 280, 1871–1873 (1998)
Walter, H., Schmidt, B., Korn, K., Vandamme, A.M., Harrer, T., Uberla, K.: Rapid, phenotypic HIV-1 drug sensitivity assay for protease and reverse transcriptase inhibitors. J. Clin. Virol. 13, 71–80 (1999)
Shafer, R.W., Kantor, R.J., Gonzales, M.J.: The Genetic Basis of HIV-1 Resistance to Reverse Transcriptase and Protease Inhibitors. AIDS Rev. 2, 211–228 (2000)
De Gruttola, V., Dix, L., D’Aquila, R., Holder, D., Phillips, A., Ait-Khaled, M., Baxter, J., Clevenbergh, P., Hammer, S., Harrigan, R., Katzenstein, D., Lanier, R., Miller, M., Para, M., Yerly, S., Zolopa, A., Murray, J., Patick, A., Miller, V., Castillo, S., Pedneault, L., Mellors, J.: The relation between baseline HIV drug resistance and response to antiretroviral therapy: re-analysis of retrospective and prospective studies using a standardized data analysis plan. Antivir. Ther. 5, 41–48 (2000)
Kuiken, C., Korber, B., Shafer, R.W.: HIV sequence databases. AIDS Rev. 5, 52–61 (2003)
Wang, D., Bloor, S., Larder, B.A.: The application of neural networks in predicting phenotypic resistance from genotypes for HIV-1 protease inhibitors. Antivir. Ther., 51–52 (2000)
Sevin, A.D., DeGruttola, V., Nijhuis, M., Schapiro, J.M., Foulkes, A.S., Para, M.F., Boucher, C.A.: Methods for investigation of the relationship between drug-susceptibility phenotype and human immunodeficiency virus type 1 genotype with applications to AIDS clinical trials group 333. J. Infect. Dis. 182, 59–67 (2000)
Beerenwinkel, N., Schmidt, B., Walter, H., Kaiser, R., Lengauer, T., Hoffmann, D., Korn, K., Selbig, J.: Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests. IEEE Intelligent Systems in Biology, 35–41 (2001)
Beerenwinkel, N., Schmidt, B., Walter, H., Kaiser, R., Lengauer, T., Hoffmann, D., Korn, K., Selbig, J.: Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc. Natl. Acad. Sci. USA 99, 8271–8276 (2002)
Cordes, F., Kaiser, R., Selbig, J.: Bioinformatics approach to predicting HIV drug resistance. Expert Rev. Mol. Diagn. 6, 207–215 (2006)
Tierney, W.M.: Improving clinical decisions and outcomes with information: a review. Int. J. Med. Inform. 62, 1–9 (2001)
Marshall, W.W., Haley, R.W.: Use of a secure Internet Web site for collaborative medical re-search. Jama 284, 1843–1849 (2000)
Schoenberg, R., Safran, C.: Internet based repository of medical records that retains patient confidentiality. Bmj 321, 1199–1203 (2000)
Mandl, K.D., Szolovits, P., Kohane, I.S.: Public standards and patients’ control: how to keep electronic medical records accessible but private. Bmj 322, 283–287 (2001)
Diffie, W., Hellman, M.: New directions in cryptography. IEEE Transactions on Information Theory, 472–492 (1976)
Rivest, R.L., Shamir, A., Adleman, L.: A method for obtaining digital signatures and public-key cryptosystems. Communications of the ACM, 120–126 (1978)
Secure Hash Standard. FIPS PUB. Federal Information Processing Standards (1995)
Beerenwinkel, N., Daumer, M., Oette, M., Korn, K., Hoffmann, D., Kaiser, R., Lengauer, T., Selbig, J., Walter, H.: Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res. 31, 3850–3855 (2003)
Sing, T., Sander, O., Beerenwinkel, N., Lengauer, T.: ROCR: visualizing classifier performance in R. Bioinformatics 21, 3940–3941 (2005)
Sirois, S., Sing, T., Chou, K.C.: HIV-1 gp120 V3 loop for structure-based drug design. Curr. Protein Pept. Sci. 6, 413–422 (2005)
Beerenwinkel, N., Sing, T., Lengauer, T., Rahnenfuhrer, J., Roomp, K., Savenkov, I., Fischer, R., Hoffmann, D., Selbig, J., Korn, K., Walter, H., Berg, T., Braun, P., Fatkenheuer, G., Oette, M., Rockstroh, J., Kupfer, B., Kaiser, R., Daumer, M.: Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinformatics 21, 3943–3950 (2005)
Beerenwinkel, N., Lengauer, T., Daumer, M., Kaiser, R., Walter, H., Korn, K., Hoffmann, D., Selbig, J.: Methods for optimizing antiviral combination therapies. Bioinformatics 19(suppl.1), 16–25 (2003)
Beerenwinkel, N., Daumer, M., Sing, T., Rahnenfuhrer, J., Lengauer, T., Selbig, J., Hoffmann, D., Kaiser, R.: Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. J. Infect. Dis. 191, 1953–1960 (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Roomp, K. et al. (2006). Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV. In: Leser, U., Naumann, F., Eckman, B. (eds) Data Integration in the Life Sciences. DILS 2006. Lecture Notes in Computer Science(), vol 4075. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11799511_16
Download citation
DOI: https://doi.org/10.1007/11799511_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-36593-8
Online ISBN: 978-3-540-36595-2
eBook Packages: Computer ScienceComputer Science (R0)