Genotypic drug resistance interpretation systems - The cutting edge of antiretroviral therapy

AIDS Reviews

Volumn 4, Issue 3, 2002, Pages 148-156

  Schmidt, Barbara ^a   Walter, Hauke ^a   Zeitler, Nina ^a   Korn, Klaus ^a  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

Algorithm; Bioinformatic technique; Drug resistance; HIV; Interpretation system

Indexed keywords

ABACAVIR; AMPRENAVIR; ANTIRETROVIRUS AGENT; ATAZANAVIR; DELAVIRDINE; DIDANOSINE; EFAVIRENZ; INDINAVIR; LAMIVUDINE; LOPINAVIR; LOPINAVIR PLUS RITONAVIR; NELFINAVIR; NEVIRAPINE; PROTEINASE INHIBITOR; RITONAVIR; RNA DIRECTED DNA POLYMERASE INHIBITOR; SAQUINAVIR; STAVUDINE; TENOFOVIR DISOPROXIL; UNCLASSIFIED DRUG; ZALCITABINE; ZIDOVUDINE;

ACCESS TO INFORMATION; ALGORITHM; ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; BIOMEDICAL ENGINEERING; CLINICAL GENETICS; CLINICAL TRIAL; COMPARATIVE STUDY; COMPUTER SYSTEM; CROSS RESISTANCE; DATA ANALYSIS; DRUG EFFECT; DRUG RESPONSE; GENOTYPE; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INFORMATION PROCESSING; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROBLEM SOLVING; REVIEW; STATISTICAL ANALYSIS; VIRUS MUTATION; VIRUS RESISTANCE; VIRUS STRAIN;

ALGORITHMS; ANTI-HIV AGENTS; COMPUTATIONAL BIOLOGY; DRUG RESISTANCE, VIRAL; DRUG THERAPY, COMBINATION; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; INTERNET; MICROBIAL SENSITIVITY TESTS; MUTATION; REVERSE TRANSCRIPTASE INHIBITORS;

EID: 0036629712     PISSN: 11396121     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (67)

1. DeGruttola V, Dix L, D'Aquila R, 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.
2. Durant J, Clevenbergh P, Halfon P, et al. Drug resistance genotyping in HIV-1 therapy: the VIRADAPT randomized controlled trial. Lancet 1999;353:2195-9.
3. Baxter J, Mayers D, Wentworth D, et al. A randomized study of antiretroviral management based on plasma genotypic antiretroviral resistance testing in patients failing therapy. CPCRA 046 Study Team. AIDS 2001;14:83-93.
4. Clevenbergh P, Durant J, Halfon P, et al. Persisting long-term benefit of genotype-guided treatment for HIV-infected patients failing HAART. The Viradapt study: week 48 follow-up. Antivir Ther 2000;5:65-70.
5. Cohen CJ, Hunt S, Sension M, et al. A randomized trial assessing the impact of phenotypic resistance testing on antiretroviral therapy. AIDS 2002;16:579-88.
6. Tural C, Ruiz L, Holtzer C, et al. Clinical utility of HIV-1 genotyping and expert advice: the Havana trial. AIDS 2000;16:209-18.
7. Cingolani A, Antinori A, Rizzo MG, et al. Usefulness of monitoring HIV drug resistance and adherence in individuals failing highly active antiretroviral therapy: a randomized study (ARGENTA). AIDS 2002;16:369-79.
8. Hirsch M, Brun-Vezinet F, D'Aquila R, et al. Antiretroviral drug resistance testing in adult HIV-1 infection: recommendations of an International AIDS Society-USA Panel. JAMA 2000;283:2417-2426.
9. The EuroGuidelines Group of HIV Resistance. Clinical and laboratory guidelines for the use of HIV-1 drug resistance testing as part of treatment management: recommendations for the European setting. AIDS 2001;15:309-20.
10. Walter H, Schmidt B, Korn K. A quality control trial for HIV-1 drug resistance testing using clinical samples. 8th CROI. Chicago, IL, USA 2001 [abstract 252].
11. Wensing A, Keulen W, Buimer M, Brambilla D, Schuurman R, Boucher C. Analysis of the world-wide evaluation study on HIV-1 genotype interpretation; ENVA-3. Antivir Ther 2001;6(Suppl 1):101.
12. Miller V, Schuurman R, Clavel F, et al. Comparison of HIV-1 drug susceptibility (phenotype) results reported by three major laboratories. Antivir Ther 2001;6(Supp 1):129.
13. Tisdale M, Kemp S, Parry N, Larder B. Rapid in vitro selection of human immunodeficiency virus type 1 resistant to 3′-thiacytidine inhibitors due to a mutation in the YMDD region of reverse transcriptase. Proc Natl Acad Sci USA 1993;90:5653-6.
14. Schinazi R, Larder B, Mellors J. Mutations in retroviral genes associated with drug resistance: 2000-2001 update. Int Antivir News 2000;8:65-92.
15. Ziermann R, Limoli K, Das K, et al. A mutation in HIV type 1 protease, N88S, that causes in vitro hypersensitivity to amprenavir. J Virol 2000;74:4414-9.
16. Shulman N, Zolopa AR, Passaro D, et al. Phenotypic hypersusceptibility to non-nucleoside reverse transcriptase inhibitors in treatment-experienced HIV-infected patients: impact on virological response to efavirenz-based therapy. AIDS 2001;15:1125-32.
17. Larder B, Kemp S, Harrigan R. Potential mechanism of sustained antiretroviral efficacy of AZT-3TC combination therapy. Science 1995;269:696-9
18. Kemp S, Shi C, Bloor S, et al. A novel polymorphism at codon 333 of HIV type 1 reverse transcriptase can facilitate dual resistance to zidovudine and L-2′,3′-dideoxy-3′-thiacytidine. J Virol 1998;72:5093-8.
19. Palmer S, Shafer R, Merigan T. Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development. AIDS 1999;13:661-7.
20. Haubrich R, Keiser P, Kemper C, et al. CCTG 575: a randomized, prospective study of phenotype testing versus standard of care for patients failing antiretroviral therapy. Antivir Ther 2001;6(Suppl 1):63.
21. Meynard J, Vray M, Morand-Joubert L, et al. Phenotypic or genotypic resistance testing for choosing antiretroviral therapy after treatment failure: a randomized trial. AIDS 2002;16:727-36.
22. Kempf D, Isaacson J, King M, et al. Identification of genotypic changes in HIV protease that correlate with reduced susceptibility to the protease inhibitor lopinavir among viral isolates from protease inhibitor-experienced patients. J Virol 2001;75:7462-9.
23. Shafer R. Genotypic testing for HIV type 1 drug resistance. Clin Microbiol Rev 2002;15:247-77.
24. Vandamme AM, Houyez F, Banhegyi D, et al. Laboratory guidelines for the practical use of HIV drug resistance tests in patient follow-up. Antivir Ther 2001;6:21-39.
25. Sevin A, DeGruttola V, Nijhuis M, et al. Methods for investigation of the relationship between drug-susceptibility phenotype and HIV type 1 genotype with applications to AIDS clinical trials group 333. J Infect Dis 2000;182:59-67.
26. 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 USA 2002;99:8271-6.
27. Beerenwinkel N, Schmidt B, Walter H, et al. Geno2pheno: interpreting genotypic HIV drug resistance tests. IEEE Intelligent Systems in Biology 2001;16:35-41.
28. Wang D, Bloor S, Larder B. The application of neural networks in predicting phenotypic resistance from genotypes for HIV-1 protease inhibitors. Antivir Ther 2000;5(Suppl 3):51-2.
29. Larder B, Wang D. Use of neural networks to define the genetic basis of HIV-1 resistance to d4T. AIDS 2000;14(Suppl 4):12.
30. Wang D, Harrigan R, Larder B. A 28-mutation neuronal network model that accurately predicts phenotypic resistance to lopinavir. Antivir Ther 2001;6(Suppl 1):105.
31. Schmit JC, Cogniaux J, Hermans P, et al. Multiple drug resistance to nucleoside analogues and non-nucleoside reverse transcriptase inhibitors in an efficiently replicating HIV type 1 patient strain. J Infect Dis 1996;174:962-8.
32. Lanier ER, Hellmann N, Scott J, et al. Determination of a clinically relevant phenotypic resistance "cutoff" for abacavir using the PhenoSense assay. 8th CROI. Chicago, IL, USA 2001 [abstract 254].
33. Miller MD, Margot NA, Lu B. Effect of Baseline Nucleoside-Associated Resistance on Response to Tenofovir DF (TDF) Therapy: Integrated Analyses of Studies 902 and 907. 9th CROI. Seattle, WA, USA 2002 [abstract 43].
34. Lu B, Hellmann N, Bates M, et al. Determination of clinical cut-offs for reduced response to tenofovir DF therapy in antiretroviral-experienced patients. Antivir Ther 2002;7:104.
35. Deeks S, Hellmann N, Grant R, et al. Novel four-drug salvage treatment regimens after failure of a HIV type 1 protease inhibitor-containing regimen: antiviral activity and correlation of baseline phenotypic drug susceptibility with virologic outcome. J Infect Dis 1999;179:1375-81.
36. Harrigan P, Hertogs K, Verbiest W, et al. Baseline HIV drug resistance profile predicts response to ritonavir-saquinavir protease inhibitor therapy in a community setting. AIDS 1999;13:1863-71.
37. Piketty C, Race E, Castiel P, et al. Efficacy of a five-drug combination including ritonavir, saquinavir and efavirenz in patients who failed on a conventional triple-drug regimen: phenotypic resistance to protease inhibitors predicts outcome of therapy. AIDS 1999;13:71-7.
38. Race E, Dam E, Obry V, Paulous S, Clavel F. Analysis of HIV cross-resistance to protease inhibitors using a rapid single-cycle recombinant virus assay for patients failing on combination therapies. AIDS 1999;13:2061-8.
39. Walter H, Schmidt B, Rascu A, et al. Phenotypic HIV-1 resistance correlates with treatment outcome of nelfinavir salvage therapy. Antivir Ther 2000;5:249-56.
40. Schulman N, Winters M, Shafer R, et al. Subtle changes in susceptibility to d4T predict virologic response to d4T monotherapy after AZT treatment. Antivir Ther 2001;6:(Suppl 1):91.
41. Marcelin A, Lamotte C, Delauguerre C, et al. Genotypic inhibitory quotient as a predictor of the virological response to a ritonavir/amprenavir-containing regimen in HIV-1 protease inhibitor-experienced patients. Antivir Ther 2002;7:87.
42. Szumiloski J, Wilson H, Jensen E, et al. Relationships between indinavir resistance and virological responses to indinavir-ritonavir-containing regimens in patients with previous protease inhibitor failure. Antivir Ther 2002;7:127.
43. min levels for response to a ritonavir boosted saquinavir salvage therapy. Antivir Ther 2002;7:81.
44. Duval X, Lamotte C, Race E, et al. Amprenavir inhibitory quotient and virological response in HIV-infected patients on an amprenavir-containing salvage regimen without or with ritonavir. Antimicrob Agents Chemother 2002;46:570-4.
45. Kempf D, Hsu A, Jiang P, et al. Response to ritonavir intensification in indinavir recipients is highly correlated with virtual inhibitory quotient. 8th CROI. Chicago, IL, USA 2001 [abstract 523].
46. Schapiro J, De Luca A, Harrigan R, et al. Resistance assay interpretation systems vary widely in method and approach. Antivir Ther 2001;6(Suppl 1):131.
47. Schmidt B, Walter H, Moschik B, et al. Simple algorithm derived from a geno-/phenotypic database to predict HIV-1 protease inhibitor resistance. AIDS 2000;14:1731-8.
48. Schmidt B, Korn K, Moschik B, Paatz C, Uberla K, Walter H. Low level of cross-resistance to amprenavir (141W94) in samples from patients pretreated with other protease inhibitors. Antimicrob Agents Chemother 2000;44:3213-6.
49. Lanier ER, Scott J, Ait-Khaled M, et al. Predicting abacavir antiviral activity using HIV-1 reverse transcriptase genotype: a comparison of 12 algorithms. Antivir Ther 2001;6(Suppl 1):103.
50. Decamps D, Masquelier B, Mamet JP, et al. A genotypic sensitivity score for amprenavir based on genotype at baseline and virological response. Antivir Ther 2001;6(Suppl 1):103.
51. Walter H, Schmidt B, Werwein M, Schwingel E, Korn K. Prediction of abacavir resistance from genotypic data: impact of zidovudine and lamivudine resistance in vitro and in vivo. Antimicrob Agents Chemother 2002;46:89-94.
52. Masquelier B, Tamalet C, Descamps D, et al. Identification of genotypic determinants of the virological response to tenofovir-including regimens in nucleoside reverse transcriptase inhibitor-experienced patients. Antivir Ther 2002;7:105.
53. Braun P, Helm M, Ehret R, et al. Predictive value of different drug resistance interpretation systems in therapy management of HIV-infected patients in daily routine. Antivir Ther 2002;7(Suppl):77.
54. Van Laethem K, De Luca A, Antinovir A, Cingolani A, Perno CF, Vandamme AM. A genotypic drug resistance interpretation algorithm that significantly predicts therapy response in HIV-1 infected patients. Antivir Ther 2002;7:123-9.
55. Harrigan PR, Montaner J, Wegner SA, et al. World-wide variation in HIV-1 phenotypic susceptibility in untreated individuals: biologically relevant values for resistance testing. AIDS 2001;15:1671-7.
56. Parkin N, Chappey C, Maroldo L, Bates M, Hellmann NS, Petropoulos CJ. Phenotypic and genotypic HIV-1 drug resistance assays provide complementary information. J Acquir Immune Defic Syndr (in press).
57. Schmidt B, Walter H, Schwingel E, et al. Comparison of different interpretation systems for genotypic HIV-1 drug resistance data. Antivir Ther 2001;6(Suppl 1):102.
58. Paulsen D, Florance A, Liao Q, et al. Comparison of HIV-1 protease inhibitor susceptibility results in viraemic protease inhibitor-experienced patient samples analysed by phenotyping and by five resistance algorithms. Antivir Ther 2002;7:93.
59. Reid C, Bassett R, Day S, et al. A dynamic rules-based interpretation system derived by an expert panel is predictive of virological failure. Antivir Ther 2002;7:91.
60. Torti C, Quirós-Roldán E, Keulen W, et al. Clinical evaluation of rule based and phenotype driven HIV-1 genotype interpretation systems: evidence from the GenPherex Study. Antivir Ther 2002;7:95.
61. Perez-Elías MJ, García-Arata I, Moreno S, et al. Baseline testing information given by a real phenotype (real Ph) or a virtual phenotype (virtual Ph) test in a randomized study (Realvirfen study): influence in final outcome. Antivir Ther 2002;7:89.
62. Emery S, Birch C, Crowe S, et al. CREST - A randomized comparison of two resistance test platforms: genotype and genotype plus VirtualPhenotype™: interim results. Antivir Ther 2002;7:116.
63. Zeitler N, Schmidt B, Korn K, et al. Determination of the optimal cut-offs for predicting the phenotype of nine different HIV drug resistance algorithms. Antivir Ther 2002;7:96.
64. DiRienzo G, DeGruttola V. Collaborative HIV resistance-response database initiatives: sample size for detection of relationships between HIV-1 genotype and HIV-1 RNA response using a non-parametric approach. Antivir Ther 2002;7:71.
65. 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;7:71.
66. Middleton T, Smith D, Larder B, Law M, Birch C. Baseline antiretroviral drug susceptibility influences treatment response in patients receiving saquinavir-enhancing therapy. HIV Clin Trials 2001;2:445-52.
67. Hammer S, Peeters M, Harrigan R, Larder B, for the ACTG 372B/D Study Team. Virtual phenotype is predictive of treatment failure in treatment-experienced patients. Antivir Ther 2001;6(Suppl 1):107.