The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
Open accessAbstract
Therapeutic success of anti-HIV therapies is limited by the development of drug resistant viruses. These genetic variants display complex mutational patterns in their pol gene, which codes for protease and reverse transcriptase, the molecular targets of current antiretroviral therapy. Genotypic resistance testing depends on the ability to interpret such sequence data, whereas phenotypic resistance testing directly measures relative in vitro susceptibility to a drug. From a set of 650 matched genotype-phenotype pairs we construct regression models for the prediction of phenotypic drug resistance from genotypes. Since the range of resistance factors varies considerably between different drugs, two scoring functions are derived from different sets of predicted phenotypes. Firstly, we compare predicted values to those of samples derived from 178 treatment-naive patients and report the relative deviance. Secondly, estimation of the probability density of 2000 predicted phenotypes gives rise to an intrinsic definition of a susceptible and a resistant subpopulation. Thus, for a predicted phenotype, we calculate the probability of membership in the resistant subpopulation. Both scores provide standardized measures of resistance that can be calculated from the genotype and are comparable between drugs. The geno2pheno system makes these genotype interpretations available via the Internet (http://www.genafor.org/).
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Cites
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Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database
Shafer, R. W., Stevenson, D., & Chan, B. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.348 · Cited by 907
Human immunodeficiency virus reverse transcriptase and protease sequence database
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DeGruttola, V., Dix, L., D'Aquila, R., Holder, D., Phillips, A., Ait-Khaled, M., Baxter, J., Clevenbergh, P., Hammer, S., Harrigan, R., et al. (2000) · Antiviral Therapy · doi:10.1177/135965350000500112 · Cited by 326
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Managing Resistance to Anti-HIV Drugs: An Important Consideration for Effective Disease Management
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Self-citation
Cited by
ROCR: visualizing classifier performance in R
Sing, T., Sander, O., Beerenwinkel, N., & Lengauer, T. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti623 · Cited by 3,200
Self-citationClinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis
Wilson, M. R., Sample, H. A., Zorn, K. C., Arevalo, S., Yu, G., Neuhaus, J., Federman, S., Stryke, D., Briggs, B., Langelier, C., et al. (2019) · New England Journal of Medicine · doi:10.1056/nejmoa1803396 · Cited by 1,067
Web Resources for HIV Type 1 Genotypic-Resistance Test Interpretation
Liu, T. F., & Shafer, R. W. (2006) · Clinical Infectious Diseases · doi:10.1086/503914 · Cited by 654
Hirsch, M. S., Günthard, H. F., Schapiro, J. M., Brun‐Vézinet, F., Clotet, B., Hammer, S. M., Johnson, V. A., Kuritzkes, D. R., Mellors, J. W., Pillay, D., et al. (2008) · Clinical Infectious Diseases · doi:10.1086/589297 · Cited by 573
Pineda-Peña, A.-C., Faria, N. R., Imbrechts, S., Libin, P., Abecasis, A. B., Deforche, K., Gómez-López, A., Camacho, R. J., de Oliveira, T., & Vandamme, A.-M. (2013) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2013.04.032 · Cited by 383
Metadata
- Authors
- Beerenwinkel, N.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-07-01
- Volume
- 31
- Issue
- 13
- Pages
- 3850-3855
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1988215875
- Cited by
- 266
- References
- 8
- FWCI
- 7.95
- Type
- journal article
- Language
- en
- Open access
- bronze
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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