How to compute which genes control drug resistance dynamics

Drug Discovery Today

Volumn 16, Issue 7-8, 2011, Pages 339-344

  Guo, Yunqian ^a   Luo, Jiangtao ^b   Wang, Jianxin ^a   Wang, Yaqun ^b   Wu, Rongling ^a,b  

^a BEIJING FORESTRY UNIVERSITY   (China)

^b PENN STATE COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIVIRAL RESISTANCE; GENE MAPPING; GENETIC REGULATION; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MATHEMATICAL ANALYSIS; QUANTITATIVE TRAIT LOCUS; REVIEW; VIRUS INFECTION; VIRUS LOAD;

COMPUTER SIMULATION; DRUG RESISTANCE, VIRAL; HUMANS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; MONTE CARLO METHOD; VIRAL LOAD; VIRUS DISEASES;

EID: 79953696507     PISSN: 13596446     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.drudis.2011.02.004     Document Type: Review

References (42)

1. S. Bonhoeffer Models of viral kinetics and drug resistance in HIV-1 infection AIDS Patient Care STDS 12 1998 769 774 (Pubitemid 28487711)
2. S. Bonhoeffer Virus dynamics and drug therapy Proc. Natl. Acad. Sci. U. S. A. 94 1999 6971 6976 (Pubitemid 27281975)
3. R.M. Ribeiro, and S. Bonhoeffer Production of resistant HIV mutants during antiretroviral therapy Proc. Natl. Acad. Sci. U. S. A. 97 2000 7681 7686 (Pubitemid 30460706)
4. S.G. Deeks Treatment of antiretroviral-drug-resistant HIV-1 infection Lancet 362 2003 2002 2011 (Pubitemid 37548427)
5. N.P. Peet Drug resistance: a growing problem Drug Discov. Today 15 2010 583 586
6. D.D. Ho Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection Nature 373 1999 123 126
7. M.A. Nowak, and R.M. May Virus Dynamics 2000 Oxford University Press
8. A.S. Perelson Modeling viral and immune system dynamics Nat. Rev. Immunol. 2 2002 28 36 (Pubitemid 37328773)
9. A.S. Perelson Decay characteristics of HIV-1-infected compartments during combination therapy Nature 387 1997 188 191 (Pubitemid 27209434)
10. A.S. Perelson HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time Science 271 1996 1582 1586 (Pubitemid 26097216)
11. S. Bonhoeffer Human immunodeficiency virus drug therapy and virus load J. Virol. 71 1997 6971 6976 (Pubitemid 27281975)
12. S. Bonhoeffer, and M.A. Nowak Pre-existence and emergence of drug resistance in HIV-1 infection Proc. R. Soc. B 264 1997 631 637 (Pubitemid 27241346)
13. L. Rong Modeling within-host HIV-1 dynamics and the evolution of drug resistance: trade-offs between viral enzyme function and drug susceptibility J. Theor. Biol. 247 2007 804 818 (Pubitemid 47081052)
14. L. Rong Emergence of HIV-1 drug resistance during antiretroviral treatment Bull. Math. Biol. 69 2007 2027 2060 (Pubitemid 47222249)
15. U. Shankarkumar HIV-1 evolution, drug resistance, and host genetics: the Indian scenario Virus Adaption Treat. 1 2009 1 4
16. J. Fellay Host genetics and HIV-1: the final phase? PLoS Pathog. 6 2010 e1001033
17. J. Fellay A whole-genome association study of major determinants for host control of HIV-1 Science 317 2007 944 947 (Pubitemid 47301321)
18. J. Fellay Common genetic variation and the control of HIV-1 in humans PLoS Genet. 5 2009 e1000791
19. S. Limou Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02) J. Infect. Dis. 199 2009 419 426
20. The International HapMap Consortium The International HapMap Project Nature 426 2003 789 794
21. R.L. Wu, and M. Lin Statistical and Computational Pharmacogenomics 2008 Chapman & Hall/CRC
22. C.-X. Ma Functional mapping of quantitative trait loci underlying the character process: a theoretical framework Genetics 161 2002 1751 1762
23. R.L. Wu, and M. Lin Functional mapping - how to map and study the genetic architecture of dynamic complex traits Nat. Rev. Genet. 7 2006 229 237 (Pubitemid 43361534)
24. J.T. Luo A differential equation model for functional mapping of a virus cell dynamic system J. Math. Biol. 65 2010 1 15
25. Z.H. Wang, and R.L. Wu A statistical model for high-resolution mapping of quantitative trait loci determining HIV dynamics Stat. Med. 23 2004 3033 3051
26. W. Zhao A nonstationary model for functional mapping of complex traits Bioinformatics 21 2005 2469 2477 (Pubitemid 40731604)
27. W. Zhao Structured antedependence models for functional mapping of multivariate longitudinal quantitative traits Stat. Appl. Mol. Genet. Biol. 2005 1136 10.2202/1544-6115
28. J. Yap Nonparametric modeling of covariance structure in functional mapping of quantitative trait loci Biometrics 65 2009 1068 1077
29. Das, K. et al. A dynamic model for genome-wide association studies. Hum. Genet. doi:10.1007/s00439-011-0960-6
30. A.P. Dempster Maximum likelihood from incomplete data via EM algorithm J. R. Stat. Soc. B 39 1977 1 38
31. E.S. Lander, and D. Botstein Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps Genetics 121 1989 185 199
32. D.P. Bertsekas Nonlinear Programming 2nd edn 2003 Athena Scientific
33. P. Bremaud Markov Chains: Gibbs Fields, Monte Carlo Simulation and Queues 1999 Springer
34. G.A. Churchill, and R.W. Doerge Empirical threshold values for quantitative trait mapping Genetics 138 1994 963 971 (Pubitemid 24337818)
35. S. Wu Multilocus linkage disequilibrium mapping of quantitative trait loci that affect HIV dynamics: a simulation approach Stat. Med. 25 2006 3826 3849 (Pubitemid 44718174)
36. S. Bonhoeffer Evidence for positive epistasis in HIV-1 Science 306 2004 1547 1550 (Pubitemid 39564948)
37. J. da Silva Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region Genetics 185 2010 293 303
38. S.F. Elena Simple genomes, complex interactions: epistasis in RNA virus Chaos 20 2010 026106
39. Z.H. Wang A statistical model to analyse quantitative trait locus interactions for HIV dynamics from the virus and human genomes Stat. Med. 25 2005 495 511
40. Y. Li A statistical model for genetic mapping of viral infection by integrating epidemiological behavior Stat. Appl. Genet. Mol. Biol. 2009 1475 10.2202/1544-6115
41. Q. Li, and R.L. Wu A multilocus model for constructing a linkage disequilibrium map in human populations Stat. Appl. Genet. Mol. Biol. 2009 1419 10.2202/1544-6115
42. J.F. Wilkins, and D. Haig What good is genomic imprinting: the function of parent-specific gene expression Nat. Rev. Genet. 4 2003 359 368 (Pubitemid 36538360)