RECall for Automated Genotypic Tropism Testing
نویسندگان
چکیده
منابع مشابه
Effects of sequence alterations on results from genotypic tropism testing.
BACKGROUND geno2pheno[coreceptor] is a bioinformatic method for genotypic tropism determination (GTD) which has been extensively validated. OBJECTIVES GTD can be affected by sequencing/base-calling variability and unreliable representation of minority populations in Sanger bulk sequencing. This study aims at quantifying the robustness of geno2pheno[coreceptor] with respect to these issues. GT...
متن کاملReliable Genotypic Tropism Tests for the Major HIV-1 Subtypes
Over the past decade antiretroviral drugs have dramatically improved the prognosis for HIV-1 infected individuals, yet achieving better access to vulnerable populations remains a challenge. The principal obstacle to the CCR5-antagonist, maraviroc, from being more widely used in anti-HIV-1 therapy regimens is that the pre-treatment genotypic "tropism tests" to determine virus susceptibility to m...
متن کاملParameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc
OBJECTIVES We analysed the impact of different parameters on genotypic tropism testing related to clinical outcome prediction in 108 patients on maraviroc (MVC) treatment. METHODS 87 RNA and 60 DNA samples were used. The viral tropism was predicted using the geno2pheno[coreceptor] and T-CUP tools with FPR cut-offs ranging from 1%-20%. Additionally, 27 RNA and 28 DNA samples were analysed in t...
متن کاملGenotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis
BACKGROUND Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4) variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS) detects...
متن کاملMinor Variant Detection at Different Template Concentrations in HIV-1 Phenotypic and Genotypic Tropism Testing
The clinical trials of maraviroc showed that treatment failure was mostly associated with lack of X4 virus detection at baseline. The detection limit for X4 in tropism assays is ill defined around 10%. In the current study, quantification of X4-tropic minority populations was assessed on artificial mixed samples and 38 clinical isolates. These mixtures were subjected to tropism "clonal genotypi...
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ژورنال
عنوان ژورنال: Journal of Clinical Microbiology
سال: 2013
ISSN: 0095-1137
DOI: 10.1128/jcm.00935-13