Estimating HIV evolutionary pathways and the genetic barrier to drug resistance

Journal of Infectious Diseases

Volumn 191, Issue 11, 2005, Pages 1953-1960

  Beerenwinkel, Niko ^a,e   Däumer, Martin ^b   Sing, Tobias ^a   Rahnenführer, Jörg ^a   Lengauer, Thomas ^a   Selbig, Joachim ^c   Hoffmann, Daniel ^d   Kaiser, Rolf ^b  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^b UNIVERSITY OF COLOGNE   (Germany)

^c MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^d CENTER OF ADVANCED EUROPEAN STUDIES AND RESEARCH CAESAR   (Germany)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIDANOSINE; LAMIVUDINE; RNA DIRECTED DNA POLYMERASE INHIBITOR; ZIDOVUDINE;

ARTICLE; CLINICAL PATHWAY; CONTROLLED STUDY; DRUG DESIGN; DRUG SUBSTITUTION; GENETIC HETEROGENEITY; GENOTYPE; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MAJOR CLINICAL STUDY; MOLECULAR EVOLUTION; MULTIDRUG RESISTANCE; MUTAGENESIS; NONHUMAN; PATHOGENESIS; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; VIRUS GENOME; VIRUS ISOLATION; VIRUS MUTATION;

ANTI-HIV AGENTS; DRUG RESISTANCE, VIRAL; EVOLUTION; HIV-1; MODELS, GENETIC; MUTATION;

EID: 18944399666     PISSN: 00221899     EISSN: None     Source Type: Journal    
DOI: 10.1086/430005     Document Type: Article

References (32)

1. Vandamme A, Van Laethem K, De Clerq E. Managing resistance to anti HIV drugs: an important consideration for effective disease management. Drugs 1999;57:337-61.
2. DeGruttola V, Dix L, D'Aquila, et al. 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 2000; 5:41-8.
3. Shafer R, Kantor R, Gonzales M. The genetic basis of HIV-1 resistance to reverse transcriptase and protease inhibitors. AIDS Rev 2000; 2:211-28.
4. D'Aquila R, Schapiro J, Brun-Vézinet F, et al. Drug resistance mutations in HIV-1. Top HIV Med 2003; 11:92-6.
5. Beerenwinkel N, Schmidt B, Walter H, et al. Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci 2002; 99:8271-6.
6. Gonzales MJ, Wu TD, Taylor J, et al. Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors. AIDS 2003; 17:791-9.
7. Wu TD, Schiffer CA, Gonzales MJ, et al. Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol 2003; 77:4836-47.
8. Sevin A, DeGruttola V, Nijhuis M, et al. 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 2000; 182:59-67.
9. Beerenwinkel N, Schmidt B, Walter H, et al. Geno2pheno: interpreting genotypic HIV drug resistance tests. IEEE Intellig Syst 2001; 16:35-41.
10. Foulkes AS, DeGruttola V. Characterizing the relationship between HIV-1 genotype and phenotype: prediction based classification. Biometrics 2002; 58:145-56.
11. De Luca A, Vendittoli M, Baldini F, et al. Construction, training and clinical validation of an inferential interpretation system for genotypic HIV-1 drug resistance based on fuzzy rules learning from virological outcomes. Antivir Ther 2002; 7(Suppl 1):71.
12. Van Laethem KAD, Antinori A, Cingolani A, Perna C, Vandamme A. A genotypic drug resistance interpretation algorithm that significantly predicts therapy response in HIV-1-infected patients. Antivir Ther 2002; 7:123-9.
13. Beerenwinkel N, Lengauer T, Däumer M, et al. Methods for optimizing antiviral combination therapies. Bioinformatics 2003; 19:i16-25.
14. DiRienzo AG, DeGruttola V, Larder B, Hertogs K. Nonparametric methods to predict HIV drug susceptibility phenotype from genotype. Stat Med 2003; 22:2785-98.
15. Shafer RW. Stanford HIV Drug Resistance Database. Available at: http: //hivdb.stanford.edu/. Accessed 1 September 2004.
16. Jeeninga R, Keulen W, Boucher C, Sanders R, Berkhout B. Evolution of AZT resistance in HIV-1: the 41-70 intermediate that is not observed in vivo has a replication defect. Virology 2001; 283:294-305.
17. Keulen W, Boucher C, Berkhout B. Nucleotide substitution patterns can predict the requirements for drug-resistance of HIV-1 proteins. Antivir Res 1996; 31:45-57.
18. Boucher C, O'Sullivan E, Mulder J, et al. Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects. J Infect Dis 1992; 165:105-10.
19. Larder B. Interactions between drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase. J Gen Virol 1994; 75:951-7.
20. Larder B, Kemp S. Multiple mutations in HIV-1 reverse transcriptase confer high-level resistance to zidovudine (AZT). Science 1989; 246:1155-8.
21. Landman R, Peytavin G, Descamps D, et al. Low genetic barrier to resistance is a possible cause of early virologic failures in once-daily regimen of abacavir, lamivudine, and tenofovir: the Tonus study [abstract 52]. In: Program and abstracts of the 11th Conference on Retroviruses and Opportunistic Infections (San Francisco). Alexandria, VA: Foundation for Retrovirology and Human Health.
22. Rhee S-Y, Gonzales M, Kantor R, Betts B, Ravela J, Shafer R. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucl Acids Res 2003; 31:298-303.
23. Desper R, Jiang F, Kallioniemi O-P, Moch H, Papadimitriou C, Schäffer A. Inferring tree models for oncogenesis from comparative genome hybridization data. J Comput Biol 1999; 6:37-51.
24. Beerenwinkel N, Rahnenführer J, Däumer M, et al. Learning multiple evolutionary pathways from cross-sectional data. In: Gusfield D, Bourne P, Istrail S, Pevzner P, Waterman M, eds. Proceedings of the 8th International Conference on Computational Molecular Biology (RECOMB 2004). San Diego: ACM Press, 2004:36-44.
25. Beerenwinkel N, Rahnenführer J, Kaiser R, Hoffman D, Selbig J, Lengauer T. Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinformatics (in press).
26. Beerenwinkel N, Rahnenführer J, Däumer M, et al. Mtreemix-mutagenetic trees mixture models. Available at: http://mtreemix.bioinf. mpi -sb.mpg.de. Accessed 1 September 2004.
27. International AIDS Society-USA. HIV drug resistance mutations. Available at: http://www.iasusa.org/resistance_mutations/. Accessed 1 September 2004.
28. Larder BA, Kemp SD, Harrigan PR. Potential mechanism for sustained antiretroviral efficacy of AZT-3TC combination therapy. Science 1995; 269:696-9.
29. Brun-Vezinet F, Boucher C, Loveday C, et al. HIV-1 viral load, phenotype, and resistance in a subset of drug-naïve participants from the Delta trial. Lancet 1997; 350:983-90.
30. Shulman NS, Hughes MD, Winters MA, et al. Subtle decreases in stavudine phenotypic susceptibility predict poor virologic response to stavudine monotherapy in zidovudine-experienced patients. J Acquir Immune Defic Syndr 2002; 31:121-7.
31. Collaboration of HIV Cohorts. Nucleoside analogue use before and during highly active antiretroviral therapy and virus load rebound. J Infect Dis 2004; 190:675-87.
32. Molina JM, Marcelin AG, Pavie J, et al. Didanosine in HIV-1-infected patients experiencing failure of antiretroviral therapy: a randomized placebo-controlled trial. J Infect Dis 2005; 191:840-7.