R W Shafer

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. ncbi Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe
    R W Shafer
    Department of Medicine, Stanford University, California 94305, USA
    J Virol 71:5441-8. 1997
  2. ncbi Genotypic testing for human immunodeficiency virus type 1 drug resistance
    Robert W Shafer
    Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California 94305, USA
    Clin Microbiol Rev 15:247-77. 2002
  3. ncbi High degree of interlaboratory reproducibility of human immunodeficiency virus type 1 protease and reverse transcriptase sequencing of plasma samples from heavily treated patients
    R W Shafer
    Division of Infectious Diseases and Center for AIDS Research, Stanford University Medical Center, Stanford, California 94305, USA
    J Clin Microbiol 39:1522-9. 2001
  4. ncbi Human immunodeficiency virus on the web: a guided tour
    R W Shafer
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, CA 94305, USA
    Clin Infect Dis 31:568-77. 2000
  5. ncbi Reproducibility of human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase sequencing of plasma samples from heavily treated HIV-1-infected individuals
    R W Shafer
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
    J Virol Methods 86:143-53. 2000
  6. ncbi Human immunodeficiency virus reverse transcriptase and protease sequence database
    R W Shafer
    Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 28:346-8. 2000
  7. ncbi Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors
    R W Shafer
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA
    J Virol 73:6197-202. 1999
  8. ncbi Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database
    R W Shafer
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, CA 94305, USA
    Nucleic Acids Res 27:348-52. 1999
  9. ncbi Multiple concurrent reverse transcriptase and protease mutations and multidrug resistance of HIV-1 isolates from heavily treated patients
    R W Shafer
    Stanford University Medical Center, California 94305, USA
    Ann Intern Med 128:906-11. 1998
  10. ncbi HIV-1 genotypic resistance patterns predict response to saquinavir-ritonavir therapy in patients in whom previous protease inhibitor therapy had failed
    A R Zolopa
    Division of Infectious Diseases and Geographical Medicine, Stanford University School of Medicine, CA 94305, USA
    Ann Intern Med 131:813-21. 1999

Detail Information

Publications92

  1. ncbi Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe
    R W Shafer
    Department of Medicine, Stanford University, California 94305, USA
    J Virol 71:5441-8. 1997
    ..Although substitutions in the HIV-1 RT gene are limited by functional constraints, variation between RT sequences demonstrates phylogenetic relationships that parallel env and gag gene variation...
  2. ncbi Genotypic testing for human immunodeficiency virus type 1 drug resistance
    Robert W Shafer
    Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California 94305, USA
    Clin Microbiol Rev 15:247-77. 2002
    ..This review describes the genetic mechanisms of HIV-1 drug resistance and summarizes published data linking individual RT and protease mutations to in vitro and in vivo resistance to the currently available HIV drugs...
  3. ncbi High degree of interlaboratory reproducibility of human immunodeficiency virus type 1 protease and reverse transcriptase sequencing of plasma samples from heavily treated patients
    R W Shafer
    Division of Infectious Diseases and Center for AIDS Research, Stanford University Medical Center, Stanford, California 94305, USA
    J Clin Microbiol 39:1522-9. 2001
    ....
  4. ncbi Human immunodeficiency virus on the web: a guided tour
    R W Shafer
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, CA 94305, USA
    Clin Infect Dis 31:568-77. 2000
    ....
  5. ncbi Reproducibility of human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase sequencing of plasma samples from heavily treated HIV-1-infected individuals
    R W Shafer
    Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
    J Virol Methods 86:143-53. 2000
    ..These results suggest that HIV-1 protease and RT sequencing of circulating plasma virus is highly reproducible but that the sensitivity at detecting mutations may be low if those mutations are present as minor variants...
  6. ncbi Human immunodeficiency virus reverse transcriptase and protease sequence database
    R W Shafer
    Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 28:346-8. 2000
    ..g., treatment history, subtype, presence of a particular mutation). A gene-specific sequence analysis program, new user-defined queries and nearly 2000 additional sequences were added in 1999...
  7. ncbi Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors
    R W Shafer
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA
    J Virol 73:6197-202. 1999
    ..Our results suggest that most treatment-associated amino acid substitutions are caused by selective drug pressure, including substitutions not previously associated with drug resistance...
  8. ncbi Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database
    R W Shafer
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, CA 94305, USA
    Nucleic Acids Res 27:348-52. 1999
    ..Users can retrieve additional data and view alignments of sequences sets meeting specific criteria (e.g., treatment history, subtype, presence of a particular mutation)...
  9. ncbi Multiple concurrent reverse transcriptase and protease mutations and multidrug resistance of HIV-1 isolates from heavily treated patients
    R W Shafer
    Stanford University Medical Center, California 94305, USA
    Ann Intern Med 128:906-11. 1998
    ..Drug resistance of HIV-1 is an obstacle to the long-term efficacy of antiretroviral therapy...
  10. ncbi HIV-1 genotypic resistance patterns predict response to saquinavir-ritonavir therapy in patients in whom previous protease inhibitor therapy had failed
    A R Zolopa
    Division of Infectious Diseases and Geographical Medicine, Stanford University School of Medicine, CA 94305, USA
    Ann Intern Med 131:813-21. 1999
    ..Tests for resistance to HIV drugs are available for clinical use; however, their predictive value has not been fully assessed...
  11. ncbi Efavirenz- and adefovir dipivoxil-based salvage therapy in highly treatment-experienced patients: clinical and genotypic predictors of virologic response
    N S Shulman
    Stanford University School of Medicine, Division of Infectious Diseases, California 94305, USA
    J Acquir Immune Defic Syndr 23:221-6. 2000
    ..To determine the impact of prior nonnucleoside reverse transcriptase inhibitor (NNRTI) therapy, genotypic resistance, and other variables on response to efavirenz (EFV)- and adefovir dipivoxil (ADV)-based salvage therapy...
  12. ncbi Hydroxyurea enhances the activities of didanosine, 9-[2-(phosphonylmethoxy)ethyl]adenine, and 9-[2-(phosphonylmethoxy)propyl]adenine against drug-susceptible and drug-resistant human immunodeficiency virus isolates
    S Palmer
    Center for AIDS Research at Stanford, Stanford University Medical Center, Stanford, California 94305 5107, USA
    Antimicrob Agents Chemother 43:2046-50. 1999
    ..In fixed combinations, both ddI and PMEA were synergistic with HU against wild-type and drug-resistant viruses...
  13. ncbi Genotypic correlates of a virologic response to stavudine after zidovudine monotherapy
    N S Shulman
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA
    J Acquir Immune Defic Syndr 27:377-80. 2001
    ..We conclude that in patients with prior ZDV treatment, those with only one ZDV mutation, particularly at position 70, can still get reasonable virologic activity from d4T. Those with more mutations are not likely to have much benefit...
  14. ncbi A 6-basepair insert in the reverse transcriptase gene of human immunodeficiency virus type 1 confers resistance to multiple nucleoside inhibitors
    M A Winters
    Center for AIDS Research at Stanford, Stanford University, Stanford, California 94305 5107, USA
    J Clin Invest 102:1769-75. 1998
    ..These results establish that inserts, like point mutations, are selected in vivo during antiretroviral therapy and provide resistance to multiple nucleoside analogs...
  15. ncbi Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay
    Amit Kapoor
    Department of Medicine, University of California, San Francisco, 94118, USA
    J Virol 78:7112-23. 2004
    ..The enhanced detection of minority drug resistance variants using a sequencing-based assay may improve the efficacy of genotype-assisted salvage therapies...
  16. ncbi Comparison of four-drug regimens and pairs of sequential three-drug regimens as initial therapy for HIV-1 infection
    Robert W Shafer
    Stanford University Medical Center, Stanford, Calif, USA
    N Engl J Med 349:2304-15. 2003
    ..It is unclear whether therapy for human immunodeficiency virus type 1 (HIV-1) should be initiated with a four-drug or two sequential three-drug regimens...
  17. ncbi Human immunodeficiency virus reverse transcriptase and protease sequence database
    Soo-Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 31:298-303. 2003
    ..Sequence data on two new molecular targets of HIV drug therapy--gp41 (cell fusion) and integrase--will be added to the database in 2003...
  18. ncbi Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations
    Yumi Mitsuya
    Department of Medicine, Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA
    J Virol 82:10747-55. 2008
    ....
  19. ncbi Human immunodeficiency virus type 1 isolates with the reverse transcriptase (RT) mutation Q145M retain nucleoside and nonnucleoside RT inhibitor susceptibility
    Vici Varghese
    Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
    Antimicrob Agents Chemother 53:2196-8. 2009
    ..We report that Q145M and other Q145 mutations do not emerge with RT inhibitors nor decrease RT inhibitor susceptibility. Q145M should not, therefore, be considered an RT inhibitor resistance mutation...
  20. ncbi HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL
    Yumi Mitsuya
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford 94305, and Kaiser-Permanente Medical Care Program-Northern California, Oakland, CA, USA
    J Acquir Immune Defic Syndr 43:56-9. 2006
    ..Genotype validity was confirmed in 49 of 50 patients with a previous or follow-up genotype. The belief that genotypic resistance testing is unreliable in samples with low-level viremia should be reassessed...
  21. ncbi Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testing
    Soo-Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
    Antimicrob Agents Chemother 48:3122-6. 2004
    ..Characterization of the phenotypic and clinical significance of these common patterns may lead to improved treatment recommendations for a large proportion of patients for whom antiretroviral therapy is failing...
  22. ncbi Phenotypic hypersusceptibility to non-nucleoside reverse transcriptase inhibitors in treatment-experienced HIV-infected patients: impact on virological response to efavirenz-based therapy
    N Shulman
    Stanford University School of Medicine, Stanford, CA 94305, USA
    AIDS 15:1125-32. 2001
    ..A reversal of phenotypic resistance was seen in patients with NNRTI mutations in the presence of multiple NRTI mutations, but no obvious virologic benefit of this phenomenon was seen in this study...
  23. ncbi Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: classification, amino acid mutation patterns, and prevalence in a northern California clinic-based population
    M J Gonzales
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA
    J Infect Dis 184:998-1006. 2001
    ..RT and protease sequences from 2246 HIV-infected persons in northern California were also examined: 99.4% of the sequences clustered with subtype B, whereas 0.6% clustered with subtype A, C, or D...
  24. ncbi HIV-1 protease and reverse transcriptase mutation patterns responsible for discordances between genotypic drug resistance interpretation algorithms
    Jaideep Ravela
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94301, USA
    J Acquir Immune Defic Syndr 33:8-14. 2003
    ..Determining the clinical significance of these mutation patterns responsible for interalgorithm discordances will improve interalgorithm concordance and the accuracy of genotypic resistance interpretation...
  25. ncbi Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients
    Severine Margeridon-Thermet
    Department of Medicine, Stanford University, Stanford, CA, USA
    J Infect Dis 199:1275-85. 2009
    ..UDPS detected low-prevalence HBV variants with NRTI-resistance mutations, G-to-A hypermutation, and low-level dual genotype infection with a sensitivity not previously possible...
  26. ncbi Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance
    Chunlin Wang
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Genome Res 17:1195-201. 2007
    ..With appropriate analysis, ultra-deep pyrosequencing is a promising method for characterizing genetic diversity and detecting minor yet clinically relevant variants in biological samples with complex genetic populations...
  27. ncbi Case files from Stanford University Medical Center: Drug resistance testing in previously untreated patients with HIV--knowing what to look for and choosing appropriate therapy
    Robert W Shafer
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
    MedGenMed 8:32. 2006
  28. ncbi Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group study
    Todd Hulgan
    Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
    AIDS 19:1341-9. 2005
    ..The objective of this study was to determine if NRTI-associated peripheral neuropathy is associated with European mitochondrial haplogroups...
  29. ncbi Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments
    Thomas D Wu
    Department of Biochemistry, Stanford University, Stanford, California 94305, USA
    J Virol 77:4836-47. 2003
    ..The presence of mutational clusters provides insight into the complex mutational patterns required for HIV-1 protease inhibitor resistance...
  30. ncbi The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance
    Robert J Gifford
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
    Bioinformatics 25:1197-8. 2009
    ..Availability: http://cpr.stanford.edu/cpr/index.html...
  31. ncbi Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations
    Elizabeth Johnston
    Division of Infectious Diseases, Stanford University, Stanford, CA, USA
    AIDS 19:731-3. 2005
    ..Testing the activity of new antiretroviral compounds against this panel of drug-resistant clones will determine their relative activity against many clinically relevant NRTI-resistant viruses...
  32. ncbi Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration
    Rami Kantor
    Division of Infectious Disease and Center for AIDS Research, Stanford University, Stanford, California, USA
    PLoS Med 2:e112. 2005
    ..The genetic differences among HIV-1 subtypes may be critical to clinical management and drug resistance surveillance as antiretroviral treatment is expanded to regions of the world where diverse non-subtype-B viruses predominate...
  33. ncbi HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance
    Soo-Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, CA 94301, USA
    J Infect Dis 192:456-65. 2005
    ..In contrast, nonpolymorphic treatment-associated mutations may be more sensitive and specific markers of transmitted HIV-1 drug resistance...
  34. ncbi Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing
    Matthew J Gonzales
    Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
    J Acquir Immune Defic Syndr 34:398-402. 2003
    ....
  35. ncbi Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation
    Matthew J Gonzales
    Department of Medicine/Division of Infectious Diseases, Stanford University, Stanford, USA
    J Infect Dis 188:397-405. 2003
    ..Although HIV-1 PR and RT genes from treated persons may become highly divergent, these changes usually are the result of sequence evolution, rather than superinfection...
  36. ncbi Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance
    Elizabeth Johnston
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    Antimicrob Agents Chemother 48:4864-8. 2004
    ..In combination with other drug resistance mutations, L23I was associated with multidrug resistance and a compensatory increase in replication capacity...
  37. ncbi HIV-1 drug resistance mutations: an updated framework for the second decade of HAART
    Robert W Shafer
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
    AIDS Rev 10:67-84. 2008
    ..CCR5 inhibitor resistance results from mutations that promote gp120 binding to an inhibitor-bound CCR5 receptor or CXCR4 tropism; however, the genotypic correlates of these processes are not yet well characterized...
  38. ncbi HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance
    Robert W Shafer
    Division of Infectious Diseases, Stanford University, Stanford, California, USA
    AIDS 21:215-23. 2007
    ..However, such programs will not produce comparable estimates unless a standardized list of drug-resistance mutations is used to define transmitted resistance...
  39. ncbi Rationale and uses of a public HIV drug-resistance database
    Robert W Shafer
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    J Infect Dis 194:S51-8. 2006
    ..Such genotype-treatment, genotype-phenotype, and genotype-outcome correlations are contained in the Stanford HIV RT and Protease Sequence Database and have specific usefulness...
  40. ncbi The HIV-1 Non-subtype B Workgroup: an international collaboration for the collection and analysis of HIV-1 non-subtype B data
    Rami Kantor
    Division of Infectious Diseases, Brown University, Providence, Rhode Island, USA
    MedGenMed 7:71. 2005
  41. ncbi Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
    Retrovirology 5:74. 2008
    ..1% of sequences--were nonpolymorphic. Several accessory INI-resistance mutations including L74M, T97A, V151I, G163R, and S230N were also polymorphic with polymorphism rates ranging between 0.5% to 2.0%...
  42. ncbi HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes
    Soo Yon Rhee
    Division of Infectious Disease, Stanford University, Stanford, California, USA
    AIDS 20:643-51. 2006
    ..As additional non-B sequences from persons with well-characterized antiretroviral treatment histories have become available, the program has been extended to subtypes A, C, D, F, G, CRF01, and CRF02...
  43. ncbi Genotypic predictors of human immunodeficiency virus type 1 drug resistance
    Soo-Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:17355-60. 2006
    ..Mutation regression coefficients showed that, within a drug class, cross-resistance patterns differ for different mutation subsets and that cross-resistance has been underestimated...
  44. ncbi Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies
    Robert W Shafer
    Division of Infectious Diseases, Stanford University, Stanford, CA, USA
    Antivir Ther 13:59-68. 2008
    ..The process used to create a previously published list of drug resistance mutations for HIV-1 surveillance is reviewed and alternative approaches to this process are discussed...
  45. ncbi Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance
    Robert J Gifford
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    AIDS 22:717-25. 2008
    ..The potential impact of undetected lethal editing on genotypic estimation of transmitted drug resistance was assessed...
  46. ncbi Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy
    Rami Kantor
    Division of Infectious Diseases and AIDS Research, Stanford University, Stanford, California 94301, USA
    Antimicrob Agents Chemother 46:1086-92. 2002
    ..The persistence of L90M, V82A/F/T, G48V, and I84V during salvage therapy suggests that these mutations play a role in clinical resistance to multiple PIs...
  47. ncbi Accuracy, precision, and consistency of expert HIV type 1 genotype interpretation: an international comparison (The GUESS Study)
    Andrew R Zolopa
    Stanford University School of Medicine, Stanford, CA 94305 5107, USA
    Clin Infect Dis 41:92-9. 2005
    ..We sought to determine how much agreement exists within a group of experts in the interpretation of complex genotypes...
  48. ncbi Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors
    Matthew J Gonzales
    Division of Infectious Diseases, Department of Medicine, Stanford University, CA, USA
    AIDS 17:791-9. 2003
    ..Most NRTI mutations group into one of three clusters, although several (e.g., M184V) occur in multiple mutational contexts...
  49. ncbi Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
    Soo Yon Rhee
    Department of Medicine, Stanford University, CA, United States
    Antiviral Res 88:269-75. 2010
    ..HBVrtDB and HBVseq are available at http://hivdb.stanford.edu/HBV/releaseNotes/...
  50. ncbi HIV-1 protease mutations and protease inhibitor cross-resistance
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    Antimicrob Agents Chemother 54:4253-61. 2010
    ....
  51. ncbi Predictive value of HIV-1 genotypic resistance test interpretation algorithms
    Soo Yon Rhee
    Division of Infectious Diseases, Dept of Medicine, Stanford University, Stanford, CA 94305, USA
    J Infect Dis 200:453-63. 2009
    ..Multiple drug-resistance interpretation algorithms have been developed, but their predictive value has rarely been evaluated using contemporary clinical data sets...
  52. ncbi Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation
    Vici Varghese
    Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
    PLoS ONE 5:e10992. 2010
    ..Several lines of evidence suggest that K65R is more common in HIV-1 subtype C than subtype B viruses...
  53. ncbi HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy
    Rami Kantor
    Division of Infectious Diseases and AIDS Research, Stanford University, California 94305, USA
    AIDS Res Hum Retroviruses 18:1407-13. 2002
    ..Comparison of subtype C RT and protease sequences with a large database of subtype B sequences identified subtype C-specific polymorphisms and candidate drug resistance mutations...
  54. ncbi Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations
    Elizabeth C Reuman
    Division of Infectious Diseases, Department of Medicine, Stanford University, 300 Pasteur Drive, Grant S 146, Stanford, CA 94305, USA
    J Antimicrob Chemother 65:1477-85. 2010
    ....
  55. ncbi Subtle decreases in stavudine phenotypic susceptibility predict poor virologic response to stavudine monotherapy in zidovudine-experienced patients
    Nancy S Shulman
    Stanford University School of Medicine, California 94305, USA
    J Acquir Immune Defic Syndr 31:121-7. 2002
    ..d4T susceptibility greater than 1.4-fold change was associated with failure to achieve significant viral load reduction after 8 weeks of d4T monotherapy...
  56. ncbi Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector
    Elizabeth C Reuman
    Department of Medicine, Stanford University School of Medicine, Division of Infectious Diseases, 300 Pasteur Drive, Grant Building, Room S 146, Stanford, CA 94305, USA
    Antimicrob Agents Chemother 54:934-6. 2010
    ..Investigational integrase inhibitors with activity against these clones are likely to retain activity against the most clinically relevant raltegravir-resistant variants...
  57. ncbi Nonnucleoside reverse transcriptase inhibitor phenotypic hypersusceptibility can be demonstrated in different assays
    Nancy S Shulman
    Center for AIDS Research, Division of Infectious Diseases, Stanford University, Stanford, CA 97305, USA
    J Acquir Immune Defic Syndr 39:78-81. 2005
    ..In fact, there was a report that a commercial multicycle assay did not readily detect hypersusceptibility...
  58. ncbi Drug resistance and antiretroviral drug development
    Robert W Shafer
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    J Antimicrob Chemother 55:817-20. 2005
    ..Clinical studies are required, however, to delineate the full spectrum of mutations responsible for resistance to a new drug and to identify the settings in which a new drug is likely to be most useful for salvage therapy...
  59. ncbi HIV-1 integrase sequence variability in antiretroviral naïve patients and in triple-class experienced patients subsequently treated with raltegravir
    Vici Varghese
    Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
    AIDS Res Hum Retroviruses 26:1323-6. 2010
    ..However, none of the major INI-resistance mutations was found to be polymorphic in either study and there were no significant changes in the prevalence of any of the minor INI-resistance mutations...
  60. ncbi Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays
    Jie Zhang
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    J Acquir Immune Defic Syndr 38:439-44. 2005
    ..CONCLUSION: The PhenoSense assay is more precise than the Antivirogram assay and superior at detecting resistance to abacavir, didanosine, and stavudine...
  61. ncbi Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations
    Rajin Shahriar
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Antimicrob Agents Chemother 53:4869-78. 2009
    ..The spectrum of treatment-selected mutations is changing as data for more individuals are collected, treatment exposures change, and the number of available sequences from non-subtype B viruses increases...
  62. ncbi Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy
    Rami Kantor
    Division of Infectious Diseases, Center for AIDS Research, Stanford University, Stanford, California, USA
    AIDS 18:1503-11. 2004
    ..The frequency with which new drug-resistance mutations (DRM) developed and their potential consequences in patients continuing unchanged treatment despite persistent viremia were assessed...
  63. ncbi Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors
    Vici Varghese
    Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
    J Acquir Immune Defic Syndr 52:309-15. 2009
    ..Therefore, we sought to determine how often NNRTI-resistant mutations other than K103N occur as minority variants in plasma samples for which standard genotypic resistance testing detects K103N alone...
  64. ncbi Case files from Stanford University Medical Center: ten years of HAART: a long wait for full HIV suppression
    Nancy Shulman
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
    MedGenMed 9:10. 2007
  65. ncbi HIV-1 subtype B protease and reverse transcriptase amino acid covariation
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, United States of America
    PLoS Comput Biol 3:e87. 2007
    ..Whereas accessory nucleoside RT inhibitor-resistance mutations nearly always follow primary nucleoside RT inhibitor-resistance mutations, accessory PI-resistance mutations often preceded primary PI-resistance mutations...
  66. ncbi Glucose metabolism, lipid, and body fat changes in antiretroviral-naive subjects randomized to nelfinavir or efavirenz plus dual nucleosides
    Michael P Dube
    Division of Infectious Diseases, Indiana University, Indianapolis, Indiana, USA
    AIDS 19:1807-18. 2005
    ..To determine if particular components of antiretroviral drug regimens are associated with greater insulin resistance, dyslipidemia, and peripheral lipoatrophy...
  67. ncbi N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure
    Yumi Mitsuya
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    AIDS Res Hum Retroviruses 22:1300-5. 2006
    ....
  68. ncbi Web resources for HIV type 1 genotypic-resistance test interpretation
    Tommy F Liu
    Division of Infectious Diseases, Stanford University, Stanford, California 94301, USA
    Clin Infect Dis 42:1608-18. 2006
    ..We describe the scientific principles of HIV-1 genotypic-resistance test interpretation and the most commonly used Web-based resources for clinicians ordering genotypic drug-resistance tests...
  69. ncbi Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy
    Asha R Kallianpur
    Department of Medicine, Divisions of General Internal Medicine and Public Health, Nashville, TN, USA
    AIDS 20:1503-13. 2006
    ..Since iron deficiency is associated with some types of PN, and iron is essential for mitochondrial function, we tested the hypothesis that hemochromatosis (HFE) gene mutations influence susceptibility to NRTI-induced PN...
  70. ncbi Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatment
    Yumi Mitsuya
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    J Infect Dis 196:1177-9. 2007
    ..Most PI-treated patients should respond favorably to DRV-based salvage therapy...
  71. ncbi Protease and reverse transcriptase mutation patterns in HIV type 1 isolates from heavily treated persons: comparison of isolates from Northern California with isolates from other regions
    Matthew J Gonzales
    Division of Infestious Diseases, Department of Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
    AIDS Res Hum Retroviruses 19:909-15. 2003
    ..The majority of clusters contained Northern California and literature sequences in similar proportions...
  72. ncbi Butting heads with resistance
    Robert W Shafer
    Stanford University School of Medicine, Stanford, California, USA
    IAPAC Mon 12:180-9. 2006
  73. ncbi Case files from Stanford University Medical Center: the initial presentation of HIV-1 infection--where public and personal health meet
    Minghsun Liu
    Division of Infectious Diseases, Stanford University Medical Center, Stanford, California, USA
    MedGenMed 8:24. 2006
  74. ncbi Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN)
    Matthew J Gonzales
    Division of Infectious Diseases, Stanford University Medical Center, 300 Pasteur Drive, Room S-156, CA 94305, USA
    Bioinformatics 18:886-7. 2002
    ..AVAILABILITY: Syn-SCAN is implemented on the web and can be downloaded from http://hivdb.stanford.edu...
  75. ncbi Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine
    Denise Lecossier
    INSERM U552, , Paris, France
    J Acquir Immune Defic Syndr 38:37-42. 2005
    ..These findings support the idea that minority viral populations with distinct resistance genotypes, although undetectable by standard genotyping, can contribute to the failure of salvage regimens...
  76. ncbi HIV sequence databases
    Carla Kuiken
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    AIDS Rev 5:52-61. 2003
    ..The types of data and services these two databases offer, the tools they provide, and the way they are set up and operated are described in detail...
  77. ncbi Algorithm specification interface for human immunodeficiency virus type 1 genotypic interpretation
    Bradley J Betts
    J Clin Microbiol 41:2792-4. 2003
  78. ncbi Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and D
    Susan H Eshleman
    Department of Pathology, Johns Hopkins Medical Institutions, Ross Building 646, 720 Rutland Avenue, Baltimore, MD 21205, USA
    AIDS Res Hum Retroviruses 18:507-11. 2002
    ..The large number of different types of pol recombinants identified suggests that recombination occurs readily in the pol region. Perinatal transmission of the recombinant viruses demonstrates their evolutionary stability...
  79. ncbi Drug resistance mutations in HIV-1
    Jonathan M Schapiro
    Vanderbilt University Medical Center, Nashville, TN, USA
    Top HIV Med 11:92-6. 2003
  80. ncbi Comparative evaluation of three computerized algorithms for prediction of antiretroviral susceptibility from HIV type 1 genotype
    Maurizio Zazzi
    Department of Molecular Biology, University of Siena, Siena, Italy
    J Antimicrob Chemother 53:356-60. 2004
    ..To compare three methods for using HIV-1 genotype to predict antiretroviral drug susceptibility...
  81. ncbi Comparison of sequential three-drug regimens as initial therapy for HIV-1 infection
    Gregory K Robbins
    Harvard Medical School, Boston, USA
    N Engl J Med 349:2293-303. 2003
    ..The optimal sequencing of antiretroviral regimens for the treatment of infection with human immunodeficiency virus type 1 (HIV-1) is unknown. We compared several different antiretroviral treatment strategies...
  82. ncbi Pharmacokinetics of nelfinavir and efavirenz in antiretroviral-naive, human immunodeficiency virus-infected subjects when administered alone or in combination with nucleoside analog reverse transcriptase inhibitors
    Patrick F Smith
    Adult ACTG Pharmacology Support Laboratory, Laboratory for Antiviral Research, Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 12460, USA
    Antimicrob Agents Chemother 49:3558-61. 2005
    ..There were no significant differences in efavirenz pharmacokinetics...
  83. ncbi Pharmacogenetics of long-term responses to antiretroviral regimens containing Efavirenz and/or Nelfinavir: an Adult Aids Clinical Trials Group Study
    David W Haas
    Vanderbilt University School of Medicine, Nashville, TN 37203, USA
    J Infect Dis 192:1931-42. 2005
    ..Nelfinavir is a substrate for P-glycoprotein, which is encoded by MDR1. The present study examined associations between genetic variants and long-term responses to treatment...
  84. ncbi Multilocus genetic interactions and response to efavirenz-containing regimens: an adult AIDS clinical trials group study
    Alison A Motsinger
    Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
    Pharmacogenet Genomics 16:837-45. 2006
    ..We examined whether long-term responses to efavirenz, and/or plasma efavirenz exposure, are better predicted by multilocus genetic interactions than by individual polymorphisms...
  85. ncbi Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
    Andre Altmann
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:169-78. 2007
    ..The virus's evolutionary potential for escaping from drug pressure is explored as an additional predictor...
  86. ncbi Virologic efficacy of boosted double versus boosted single protease inhibitor therapy
    Maya L Petersen
    Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
    AIDS 21:1547-54. 2007
    ..We compared the probability of attaining an undetectable HIV RNA level after using either boosted double or boosted single PI regimens...
  87. ncbi Educational attainment and response to HAART during initial therapy for HIV-1 infection
    Linda G Marc
    Cornell HIV Clinical Trials Unit, New York, NY, USA
    J Psychosom Res 63:207-16. 2007
    ....
  88. ncbi World Antimalarial Resistance Network (WARN) III: molecular markers for drug resistant malaria
    Christopher V Plowe
    Center for Vaccine Development, University of Maryland School of Medicine, 685 West Baltimore Street, HSF1 480, Baltimore, Maryland 21201, USA
    Malar J 6:121. 2007
    ....
  89. ncbi Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients
    Amit Kapoor
    Blood Systems Research Institute, San Francisco, CA 94118, USA
    Retrovirology 5:7. 2008
    ....
  90. ncbi Effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy in HIV-1-positive subjects: results from ACTG 384
    Rajesh T Gandhi
    Massachusetts General Hospital, Boston, MA, USA
    J Acquir Immune Defic Syndr 42:426-34. 2006
    ..To assess the effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy (ART)...
  91. ncbi Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent
    Joke Snoeck
    Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium
    Antimicrob Agents Chemother 50:694-701. 2006
    ..It is not yet known whether therapy response is subtype dependent, but the advice given to clinicians based on a genotypic interpretation algorithm differs according to the subtype...
  92. ncbi Reverse transcriptase and protease sequence evolution in two HIV-1-infected couples
    Sarah Palmer
    HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702 1201, USA
    J Acquir Immune Defic Syndr 31:285-90. 2002
    ....