Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase

AIDS Research and Human Retroviruses

Volumn 28, Issue 8, 2012, Pages 894-901

  Delong, Allison K ^a   Wu, Mingham ^b   Bennett, Diane ^c   Parkin, Neil ^d   Wu, Zhijin ^a   Hogan, Joseph W ^a   Kantor, Rami ^e  

^a BROWN UNIVERSITY   (United States)

^b CardioDx Inc   (United States)

^c CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^d DATA FIRST CONSULTING INC   (United States)

^e BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; RNA DIRECTED DNA POLYMERASE;

AMINO ACID SEQUENCE; ANALYTICAL EQUIPMENT; ARTICLE; DNA SEQUENCE; GENE MUTATION; HISTOGRAM; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; QUALITY CONTROL; SEQUENCE ANALYSIS; STOP CODON;

BASE SEQUENCE; DRUG RESISTANCE, VIRAL; HIV INFECTIONS; HIV PROTEASE; HIV REVERSE TRANSCRIPTASE; HIV-1; PEPTIDE HYDROLASES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84864248957     PISSN: 08892229     EISSN: 19318405     Source Type: Journal    
DOI: 10.1089/aid.2011.0120     Document Type: Article

References (48)

1. Joint United Nations Programme on HIV/AIDS (UNAIDS) and World Health Organization (WHO). AIDS epidemic update: 2007. http://www.unaids.org/en/HIV- data/ 2007EpiUpdate/default.asp.
2. Palella FJ Jr, Delaney KM, Moorman AC, et al.: Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators. N Engl J Med 1998;338(13):853-860.
3. Hirsch MS, Gunthard HF, Schapiro JM, et al.: Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis 2008;47(2):266-285.
4. DHHS Panel on Antiretroviral Guidelines for Adults and Adolescents-A Working Group of the Office of AIDS Research Advisory Council (OARAC). Guidelines for the use of antiretroviral agents in HIV-1 infected adults and adolescents. http://www.aidsinfo.nih.gov/guidelines.
5. Richman DD, Morton SC, Wrin T, et al.: The prevalence of antiretroviral drug resistance in the United States. AIDS 2004;18(10):1393-1401.
6. Little SJ, Holte S, Routy JP, et al.: Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med 2002;347(6):385-394.
7. McCutchan FE: Global epidemiology of HIV. J Med Virol 2006;78(Suppl 1):S7-S12.
8. Hemelaar J, Gouws E, Ghys PD, and Osmanov S: Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004. AIDS 2006;20(16):W13-23.
9. Kantor R: Impact of HIV-1 pol diversity on drug resistance and its clinical implications. Curr Opin Infect Dis 2006;19(6): 594-606.
10. Kantor R, Katzenstein D, Efron B, et al.: Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotypic evolution: Results of a global collaboration. PLOS Med 2005;2:e112.
11. Brenner B, Turner D, Oliveira M, et al.: A V106M mutation in HIV-1 clade C viruses exposed to efavirenz confers crossresistance to non-nucleoside reverse transcriptase inhibitors. AIDS 2003;17(1):F1-5.
12. Brenner BG, Oliveira M, Doualla-Bell F, et al.: HIV-1 subtype C viruses rapidly develop K65R resistance to tenofovir in cell culture. AIDS 2006;20(9):F9-F13.
13. Grossman Z, Sugarman K, Auerbuch D, et al.: Reverse transcriptase T69 6-bo insertion and multi-class resistance within a population of nucleoside reverse transcriptase inhibitor-treated subtype C patients. Antivir Ther 2002; 7(Suppl 1):S194.
14. Saravanan S, Vidya M, Balakrishanan P, et al.: Evaluation of two human immunodeficiency virus-1 genotyping systems: ViroSeq 2.0 and an in-house method. J Virol Methods 2009;159(2):211-216.
15. U.S. Food and Drug Administration. FDA licensed and approved HIV tests. http://www.fda.gov/ohrms/dockets/ac/03/ briefing/3982b1-Licensed- Approved%20HIV%20Tests.doc.
16. Land S, Cunningham P, Zhou J, et al.: TREAT Asia Quality Assessment Scheme (TAQAS) to standardize the outcome of HIV genotypic resistance testing in a group of Asian laboratories. J Virol Methods 2009;159(2):185-193.
17. Galli RA, Sattha B, Wynhoven B, et al.: Sources and magnitude of intralaboratory variability in a sequence-based genotypic assay for human immunodeficiency virus type 1 drug resistance. J Clin Microbiol 2003;41(7):2900-2907.
18. Huang DD, Eshleman SH, Brambilla DJ, et al.: Evaluation of the editing process in human immunodeficiency virus type 1 genotyping. J Clin Microbiol 2003;41(7):3265-3272.
19. Gene Codes Corporation. Sequencher 4.10.1. DNA Sequence Assembly Software: For Mac and Windows.
20. Ewing B, Hillier L, Wendl MC, and Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998;8(3):175-185.
21. Korber B and Myers G: Signature pattern analysis: A method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses 1992;8:1549-1560.
22. Boeri E, Canducci F, Grasso MA, et al.: Phylogenetic internal control for HIV-1 genotypic antiretroviral testing. New Microbiol 2004;27(2 Suppl 1):105-109.
23. Learn GH Jr, Korber BT, Foley B, et al.: Maintaining the integrity of human immunodeficiency virus sequence databases. J Virol 1996;70:5720-5730.
24. Kjaer J and Ledergerber B: HIV cohort collaborations: Proposal for harmonization of data exchange. Antivir Ther 2004;9(4):631-633.
25. Larkin MA, Blackshields G, Brown NP, et al.: Clustal W and Clustal X version 2.0. Bioinformatics 2007;23(21):2947-2948.
26. Edgar RC: MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32(5): 1792-1797.
27. Korber B: HIV signature and sequence variation analysis. In: Computational and Evolutionary Analysis of HIV Molecular Sequences (Rodrigo AG, Learn GH, Eds.). Kluwer Academic Publishers, Dordrecht, The Netherlands, 2000, pp. 55-72.
28. Los Alamos HIV Database. www.hiv.lanl.gov. http://www .hiv.lanl.gov/content/index.
29. Liu TF and Shafer RW: Web resources for HIV type 1 genotypic- resistance test interpretation. Clin Infect Dis 2006; 42(11):1608-1618.
30. Sturmer M, Doerr HW, and Preiser W: Variety of interpretation systems for human immunodeficiency virus type 1 genotyping: Confirmatory information or additional confusion? Curr Drug Targets Infect Disord 2003;3(4):373-382.
31. Kantor R, Machekano R, Gonzales MJ, et al.: Human immunodeficiency virus reverse transcriptase and protease sequence database: An expanded model integrating natural language text and sequence analysis. Nucleic Acids Res 2001;29:296-299.
32. Rhee SY, Gonzales MJ, Kantor R, et al.: Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 2003;31(1):298-303.
33. Shafer RW, Jung DR, and Betts BJ: Human immunodeficiency virus type 1 reverse transcriptase and protease mutation search engine for queries. Nat Med 2000;6(11): 1290-1292.
34. Shafer RW, Jung DR, Betts BJ, et al.: Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 2000;28:346-348.
35. Shafer RW, Stevenson D, and Chan B: Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 1999;27:348-352.
36. R: A language and environment for statistical computing [computer program]. Version. Vienna, Austria: http://www .R-project.org; 2009.
37. Perl. Programming language. http://www.perl.org/.
38. Gonzales MJ, Dugan JM, and Shafer RW: Synonymous-nonsynonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). Bioinformatics 2002; 18(6):886-887.
39. Paradis E, Claude J, and Strimmer K: APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 2004;20(2):289-290.
40. FASTA. Sequence Format. http://www.ncbi.nlm.nih.gov/ BLAST/fasta.shtml.
41. Huang X and Zhang J: Methods for comparing a DNA sequence with a protein sequence. Comput Appl Biosci 1996;12(6):497-506.
42. Johnson VA, Brun-Vezinet F, Clotet B, et al.: Update of the drug resistance mutations in HIV-1: December 2009. Top HIV Med 2009;17(5):138-145.
43. Bennett DE, Bertagnolio S, Sutherland D, and Gilks CF: The World Health Organization's global strategy for prevention and assessment of HIV drug resistance. Antivir Ther 2008; 13(Suppl 2):1-13.
44. Bennett DE, Myatt M, Bertagnolio S, et al.: Recommendations for surveillance of transmitted HIV drug resistance in countries scaling up antiretroviral treatment. Antivir Ther 2008;13(Suppl 2):25-36.
45. Jordan MR, Bennett DE, Bertagnolio S, et al.: World Health Organization surveys to monitor HIV drug resistance prevention and associated factors in sentinel antiretroviral treatment sites. Antivir Ther 2008;13(Suppl 2):15-23.
46. Genbank. http://www.ncbi.nlm.nih.gov/.
47. Hughes CA, Robinson L, Tseng A, and MacArthur RD: New antiretroviral drugs: A review of the efficacy, safety, pharmacokinetics, and resistance profile of tipranavir, darunavir, etravirine, rilpivirine, maraviroc, and raltegravir. Expert Opin Pharmacother 2009;10(15):2445-2466.
48. Bhattacharya S and Osman H: Novel targets for anti-retroviral therapy. J Infect 2009;59(6):377-386.