Characterizing classes of antiretroviral drugs by genotype

Statistics in Medicine

Volumn 22, Issue 16, 2003, Pages 2637-2655

  Foulkes, A S ^a   DeGruttola, V ^b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Classification; Cluster analysis; Genetic pattern; Genotype; HIV 1; Multivariate; Phenotype; Prediction

Indexed keywords

ANTIRETROVIRUS AGENT; INDINAVIR; NELFINAVIR; PROTEINASE;

ARTICLE; CLUSTER ANALYSIS; DRUG CLASSIFICATION; DRUG RESPONSE; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IN VITRO STUDY; MULTIVARIATE ANALYSIS; PHENOTYPE; PREDICTION; SEQUENCE ANALYSIS; STATISTICAL MODEL; STATISTICS;

AMINO ACID SEQUENCE; ANTI-HIV AGENTS; CLUSTER ANALYSIS; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; INDINAVIR; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; NELFINAVIR;

EID: 0041565368     PISSN: 02776715     EISSN: None     Source Type: Journal    
DOI: 10.1002/sim.1465     Document Type: Article

References (18)

1. Foulkes AS, DeGruttola V. Characterizing the relationship between hiv-1 genotype and phenotype: prediction based classification. Biometrics 2002; 58:145-156.
2. Sevin A, De Gruttola V, Nijhuis M, Schapiro JM, Foulkes AS, Para MF, Boucher CAB. Evaluating the relationship between drug susceptibility phenotype and genotype among hiv from patients treated with protease inhibitors. Journal of Infectious Diseases 2000; 182:59-67.
3. Hastie T, Tibshirani R, Eisen M, Alizadeh A, Levy R, Staudt L, Chan W, Botstein D, Brown P. 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biology 2000; 1(2):research0003.1-0003.21.
4. Zhang H, Yu C, Singer B, Xiong M. Recursive partitioning for tumor classification with gene expression microarray data. Proceedings of the National Academy of Science 2001; 98(12):6730-6735.
5. Segal MR, Cummings MP, Hubbard AE. Relating amino acid sequence to phenotype: analysis of peptide-binding data. Biometrics 2001; 57:632-643.
6. Segal M. Tree-structured methods for longitudinal data. Journal of the American Statistical Association 1992; 87(418):407-418.
7. Shafer R. The Stanford hiv rt and protease sequence database. At http://hivdb.stanford.edu/hiv/, 2001.
8. Hartigan JA. Clustering Algorithms. Wiley: 1975.
9. Tibshirani R, Walther G, Hastie T. Estimating the number of clusters in a dataset via the gap statistic. Journal of the Royal Statistical Society, Series B 2001; 32:411-423.
10. Harville D. Extension of the Gauss-Markov theorem to include the estimation of random effects. Annals of Statistics 1976; 4:384-395.
11. Breiman L, Friedman J, Olshen R, Stone C. Classification and Regression Trees. Wadsworth: 1984.
12. Zhang D, Davidian M. Linear mixed models with flexible distribution of random effects for longitudinal data. Biometrics 2001; 57(3):795-802.
13. Self SG, Liang LY. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. Journal of the American Statistical Association 1987; 82(398):605-610.
14. Molla A, Korneyeva M, Gao Q, Vasavanonda S, Schipper PJ, Mo HM, Markowitz M, Chernyavskiy T, Niu P, Lyons N, Hsu A, Granneman GR, Ho DD, Boucher CA, Leonard JM, Norbeck DW, Kempf DJ. Ordered accumulation of mutations in hiv protease confers resistance to ritonavir. National Medicine 1996; 2(7): 760-766.
15. Lachenbruch PA. Discriminant Analysis. Hafner: New York, 1975.
16. Robinson LH, Gale CV, Kleim JP. The five-prime hiv assay: a new method of generating infectious virus for drug susceptibility phenotyping. Antiviral Therapy 2000; 5(Supplement 3):101.
17. Markowitz M, Conant M, Hurley A, Schluger R, Duran M, Peterkin J, Chapman S, Patick A, Hendricks A, Yuen GJ, Hoskins W, Clendeninn N, Ho DD. A preliminary evaluation of nelfinavir mesylate, an inhibitor of human immunodeficiency virus (hiv)-1 protease, to treat hiv infection. Journal of Infectious Diseases 177(6): 1533-1540.
18. Condra J, Holder D, Schleif W, Blahy O, Danovich R, Gabryelski L, Graham D, Laird D, Quintero J, Rhodes A, Robbins H, Roth E, Shivaprakash M, Yang T, Chodakeqitz J, Deutsch P, Leavitt R, Massari R, Mellors J, Squires K, Steigbigel R, Teppler H, Emini E. Genetic correlates of in vivo viral resistance to indinavir, a human immunodeficiency virus type 1 protease inhibitor. Journal of Virology 1996; 70(12):8270-8276.