The Calibrated Population Resistance Tool: Standardized Genotypic Estimation of Transmitted HIV-1 Drug Resistance

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2009 Mar 24

PMID 19304876

Citations 94

Authors

Robert J Gifford

Tommy F Liu

Soo-Yon Rhee

Mark Kiuchi

Stephane Hue

Deenan Pillay

Robert W Shafer

Affiliations

Soon will be listed here.

Abstract

Unlabelled: The calibrated population resistance (CPR) tool is a web-accessible program for performing standardized genotypic estimation of transmitted HIV-1 drug resistance. The program is linked to the Stanford HIV drug resistance database and can additionally perform viral genotyping and algorithmic estimation of resistance to specific antiretroviral drugs.

Availability: http://cpr.stanford.edu/cpr/index.html.

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References

Huang X, Zhang J . Methods for comparing a DNA sequence with a protein sequence. Comput Appl Biosci. 1996; 12(6):497-506. DOI: 10.1093/bioinformatics/12.6.497. View

. Evidence of a decline in transmitted HIV-1 drug resistance in the United Kingdom. AIDS. 2007; 21(8):1035-9. DOI: 10.1097/QAD.0b013e3280b07761. View

. Transmission of drug-resistant HIV-1 in Europe remains limited to single classes. AIDS. 2008; 22(5):625-35. DOI: 10.1097/QAD.0b013e3282f5e062. View

Gifford R, Rhee S, Eriksson N, Liu T, Kiuchi M, Das A . Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS. 2008; 22(6):717-25. PMC: 2946849. DOI: 10.1097/QAD.0b013e3282f5e07a. View

Myers R, Gale C, Harrison A, Takeuchi Y, Kellam P . A statistical model for HIV-1 sequence classification using the subtype analyser (STAR). Bioinformatics. 2005; 21(17):3535-40. DOI: 10.1093/bioinformatics/bti569. View

Bennett D, Bertagnolio S, Sutherland D, Gilks C . The World Health Organization's global strategy for prevention and assessment of HIV drug resistance. Antivir Ther. 2008; 13 Suppl 2:1-13. View

Bertagnolio S, Soto-Ramirez L, Pilon R, Rodriguez R, Viveros M, Fuentes L . HIV-1 drug resistance surveillance using dried whole blood spots. Antivir Ther. 2007; 12(1):107-13. View

Pillay D . Current patterns in the epidemiology of primary HIV drug resistance in North America and Europe. Antivir Ther. 2004; 9(5):695-702. View

Kuritzkes D, Lalama C, Ribaudo H, Marcial M, Meyer 3rd W, Shikuma C . Preexisting resistance to nonnucleoside reverse-transcriptase inhibitors predicts virologic failure of an efavirenz-based regimen in treatment-naive HIV-1-infected subjects. J Infect Dis. 2008; 197(6):867-70. DOI: 10.1086/528802. View

10.

Gilks C, Crowley S, Ekpini R, Gove S, Perriens J, Souteyrand Y . The WHO public-health approach to antiretroviral treatment against HIV in resource-limited settings. Lancet. 2006; 368(9534):505-10. DOI: 10.1016/S0140-6736(06)69158-7. View

11.

Shafer R, Rhee S, Bennett D . Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies. Antivir Ther. 2008; 13 Suppl 2:59-68. PMC: 4388302. View

12.

Shafer R, Rhee S, Pillay D, Miller V, Sandstrom P, Schapiro J . HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS. 2007; 21(2):215-23. PMC: 2573394. DOI: 10.1097/QAD.0b013e328011e691. View

13.

Bennett D, Myatt M, Bertagnolio S, Sutherland D, Gilks C . Recommendations for surveillance of transmitted HIV drug resistance in countries scaling up antiretroviral treatment. Antivir Ther. 2008; 13 Suppl 2:25-36. View

14.

Holmes R, Malim M, Bishop K . APOBEC-mediated viral restriction: not simply editing?. Trends Biochem Sci. 2007; 32(3):118-28. DOI: 10.1016/j.tibs.2007.01.004. View

15.

Little S, Holte S, Routy J, Daar E, Markowitz M, Collier A . Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med. 2002; 347(6):385-94. DOI: 10.1056/NEJMoa013552. View

16.

Yerly S, von Wyl V, Ledergerber B, Boni J, Schupbach J, Burgisser P . Transmission of HIV-1 drug resistance in Switzerland: a 10-year molecular epidemiology survey. AIDS. 2007; 21(16):2223-9. DOI: 10.1097/QAD.0b013e3282f0b685. View

17.

Liu T, Shafer R . Web resources for HIV type 1 genotypic-resistance test interpretation. Clin Infect Dis. 2006; 42(11):1608-18. PMC: 2547473. DOI: 10.1086/503914. View

18.

Rhee S, Gonzales M, Kantor R, Betts B, Ravela J, Shafer R . Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 2003; 31(1):298-303. PMC: 165547. DOI: 10.1093/nar/gkg100. View