scholarly journals DETERMINATION OF VIRAL TROPISM BY GENOTYPING AND PHENOTYPING ASSAYS IN BRAZILIAN HIV-1-INFECTED PATIENTS

2014 ◽  
Vol 56 (4) ◽  
pp. 287-290
Author(s):  
Liã Bárbara Arruda ◽  
Marilia Ladeira de Araújo ◽  
Maira Luccia Martinez ◽  
Claudio Roberto Gonsalez ◽  
Alberto José da Silva Duarte ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Dna Sequences ◽  
False Positive Rate ◽  
Coreceptor Usage ◽  
Viral Strain ◽  
Positive Rate ◽  
Ccr5 Antagonists ◽  
Virus Strains ◽  
Hiv 1

The clinical application of CCR5 antagonists involves first determining the coreceptor usage by the infecting viral strain. Bioinformatics programs that predict coreceptor usage could provide an alternative method to screen candidates for treatment with CCR5 antagonists, particularly in countries with limited financial resources. Thus, the present study aims to identify the best approach using bioinformatics tools for determining HIV-1 coreceptor usage in clinical practice. Proviral DNA sequences and Trofile results from 99 HIV-1-infected subjects under clinical monitoring were analyzed in this study. Based on the Trofile results, the viral variants present were 81.1% R5, 21.4% R5X4 and 1.8% X4. Determination of tropism using a Geno2pheno[coreceptor] analysis with a false positive rate of 10% gave the most suitable performance in this sampling: the R5 and X4 strains were found at frequencies of 78.5% and 28.4%, respectively, and there was 78.6% concordance between the phenotypic and genotypic results. Further studies are needed to clarify how genetic diversity amongst virus strains affects bioinformatics-driven approaches for determining tropism. Although this strategy could be useful for screening patients in developing countries, some limitations remain that restrict the wider application of coreceptor usage tests in clinical practice.

scholarly journals Evaluation of the Genotypic Prediction of HIV-1 Coreceptor Use versus a Phenotypic Assay and Correlation with the Virological Response to Maraviroc: the ANRS GenoTropism Study

2010 ◽  
Vol 54 (8) ◽  
pp. 3335-3340 ◽  
Author(s):  
Patricia Recordon-Pinson ◽  
Cathia Soulié ◽  
Philippe Flandre ◽  
Diane Descamps ◽  
Mouna Lazrek ◽  
...  
Keyword(s):  
Virological Response ◽  
False Positive Rate ◽  
Baseline Viral Load ◽  
Phenotypic Assay ◽  
Sensitivity Score ◽  
Positive Rate ◽  
Set Up ◽  
Genotypic Sensitivity Score ◽  
The Relationship ◽  
Hiv 1

ABSTRACT Genotypic algorithms for prediction of HIV-1 coreceptor usage need to be evaluated in a clinical setting. We aimed at studying (i) the correlation of genotypic prediction of coreceptor use in comparison with a phenotypic assay and (ii) the relationship between genotypic prediction of coreceptor use at baseline and the virological response (VR) to a therapy including maraviroc (MVC). Antiretroviral-experienced patients were included in the MVC Expanded Access Program if they had an R5 screening result with Trofile (Monogram Biosciences). V3 loop sequences were determined at screening, and coreceptor use was predicted using 13 genotypic algorithms or combinations of algorithms. Genotypic predictions were compared to Trofile; dual or mixed (D/M) variants were considered as X4 variants. Both genotypic and phenotypic results were obtained for 189 patients at screening, with 54 isolates scored as X4 or D/M and 135 scored as R5 with Trofile. The highest sensitivity (59.3%) for detection of X4 was obtained with the Geno2pheno algorithm, with a false-positive rate set up at 10% (Geno2pheno10). In the 112 patients receiving MVC, a plasma viral RNA load of <50 copies/ml was obtained in 68% of cases at month 6. In multivariate analysis, the prediction of the X4 genotype at baseline with the Geno2pheno10 algorithm including baseline viral load and CD4 nadir was independently associated with a worse VR at months 1 and 3. The baseline weighted genotypic sensitivity score was associated with VR at month 6. There were strong arguments in favor of using genotypic coreceptor use assays for determining which patients would respond to CCR5 antagonist.

scholarly journals CRISPRIdentify: Identification of CRISPR arrays using machine learning approach

2020 ◽  
Author(s):  
Alexander Mitrofanov ◽  
Omer S. Alkhnbashi ◽  
Sergey A. Shmakov ◽  
Kira S. Makarova ◽  
Eugene V. Koonin ◽  
...  
Keyword(s):  
Machine Learning ◽  
Dna Sequences ◽  
False Positive Rate ◽  
Scoring Function ◽  
Protein S ◽  
Genomic Region ◽  
Immune Functions ◽  
Crispr Array ◽  
Positive Rate ◽  
Data Driven Approach

CRISPR-Cas are adaptive immune systems that degrade foreign genetic elements in archaea and bacteria. In carrying out their immune functions, CRISPR-Cas systems heavily rely on RNA components. These CRISPR (cr) RNAs are repeat-spacer units that are produced by processing of pre-crRNA, the transcript of CRISPR arrays, and guide Cas protein(s) to the cognate invading nucleic acids, enabling their destruction. Several bioinformatics tools have been developed to detect CRISPR arrays based solely on DNA sequences, but all these tools employ the same strategy of looking for repetitive patterns, which might correspond to CRISPR array repeats. The identified patterns are evaluated using a fixed, built-in scoring function, and arrays exceeding a cut-off value are reported. Here, we instead introduce a data-driven approach that uses machine learning to detect and differentiate true CRISPR arrays from false ones based on several features. Our CRISPR detection tool, CRISPRIdentify, performs three steps: detection, feature extraction and classification based on manually curated sets of positive and negative examples of CRISPR arrays. The identified CRISPR arrays are then reported to the user accompanied by detailed annotation. We demonstrate that our approach identifies not only previously detected CRISPR arrays, but also CRISPR array candidates not detected by other tools. Compared to other methods, our tool has a drastically reduced false-positive rate. In contrast to the existing tools, our approach not only provides the user with the basic statistics on the identified CRISPR arrays but also produces a certainty score as a practical measure of the likelihood that a given genomic region is a CRISPR array.

scholarly journals PO 8411 MOLECULAR CHARACTERISATION OF GP41 AND GP120 V3 LOOP IN HIV-1C PATIENTS FAILING SALVAGE THERAPY IN BOTSWANA

2019 ◽  
Vol 4 (Suppl 3) ◽  
pp. A34.1-A34
Author(s):  
Nokuthula S Ndlovu ◽  
Kaelo Seatla
Keyword(s):  
Viral Entry ◽  
Salvage Therapy ◽  
False Positive Rate ◽  
V3 Loop ◽  
Coreceptor Usage ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Global Challenge ◽  
Cxcr4 Coreceptor ◽  
Hiv 1

BackgroundTriple class drug-resistant HIV-1 infection remains a global challenge in individuals with extensive antiretroviral treatment (ART) experience, in terms of high mortality and probability of onward transmission. New therapeutic options within old and new drug classes are therefore essential. We determined if patients failing salvage therapy in Botswana are eligible for maraviroc (MVC) and enfuvirtide (T20) viral entry inhibitors based on the coreceptor usage and drug-resistant mutations in envelope gp120 and gp41.MethodsA total of 38 deep salvage patients were included in the analysis. We amplified and sequenced gp41 and V3 regions of HIV-1 envelope. Drug resistance mutations were analysed according to the IAS-USA 2017 reference mutation lists. Coreceptor usage was determined using PSSM and Geno2Pheno using a false-positive rate (FPR) of 10%.ResultsAmong 38 participants, 34 (89%) were successfully sequenced and amplified gp41 and 26 (68%) gp120 V3 loop sequences were obtained. Major T20 mutation G36S was obtained in 1/34 samples (5.8%) within the study population. Polymorphisms I169V(97%), I135L(100%), E151A(70.6%) and N42S(70.6%) were detected in HR1 and HR2 of gp41. CXCR4 coreceptor associated use, mutation L34M in gp41 HR1 was detected in 2 samples (5%). Analysis of coreceptor usage showed (17/26) 65.4% use of CCR5, and a (9/26) 34.6% use of the CXCR4 coreceptor.ConclusionA moderately high proportion of treatment-experienced (deep salvage) participants had CXCR4 coreceptor using strains. The use of maraviroc in Botswana would require coreceptor tropism testing. Non-T20 treatment experience in Botswana reduces the prevalence of the major mutations that confer resistance to the drug. T20 is therefore a potential alternative drug for patients failing salvage therapy in Botswana.

scholarly journals HIV-1 Tropism Test Evaluation: Assessment and Clinical Implications

ISRN Virology ◽  
2014 ◽  
Vol 2014 ◽  
pp. 1-6
Author(s):  
Stefania Chiappetta ◽  
Manuela Pogliaghi ◽  
Marco Ripa ◽  
Adriano Lazzarin ◽  
Giuseppe Tambussi ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Virological Failure ◽  
Host Cells ◽  
Clinical Implications ◽  
Test Evaluation ◽  
Coreceptor Usage ◽  
Viral Tropism ◽  
Phenotypic Assay ◽  
Specific Host ◽  
Hiv 1

CCR5 and CXCR4 chemokines receptors are critical coreceptors for the binding of HIV to specific host cells. Guidelines recommend its assessment in case of virological failure or before prescription of CCR5 inhibitors. Strategies to assess viral tropism may be divided into phenotypic and genotypic assays; registrative trials of CCR5 inhibitors used phenotypic assay, but recently genotypic ones have been used in clinical practice. The presence of CXCR4 is increasing in naïve patients, with both acute and chronic HIV-1 infections; this coreceptor usage is associated with CD4 depletion. The assessment of viral tropism should be considered in every stage of HIV-1 infection.

scholarly journals The lowest X4 Geno2Pheno false-positive rate is associated with greater CD4 depletion in HIV-1 infected patients

2012 ◽  
Vol 18 (8) ◽  
pp. E289-E298 ◽  
Author(s):  
M.M. Santoro ◽  
D. Armenia ◽  
L. Fabeni ◽  
M. Santoro ◽  
C. Gori ◽  
...  
Keyword(s):  
False Positive ◽  
False Positive Rate ◽  
Positive Rate ◽  
Hiv 1

scholarly journals Noninvasive Detection of Cocaine and Heroin Use with Single Fingerprints: Determination of an Environmental Cutoff

2018 ◽  
Vol 64 (6) ◽  
pp. 909-917 ◽  
Author(s):  
Mahado Ismail ◽  
Derek Stevenson ◽  
Catia Costa ◽  
Roger Webb ◽  
Marcel de Puit ◽  
...  
Keyword(s):  
Drug Testing ◽  
Drug Users ◽  
False Positive Rate ◽  
Heroin Use ◽  
Before And After ◽  
Secondary Transfer ◽  
Positive Rate ◽  
Testing Protocols ◽  
Drug Free

Abstract BACKGROUND Recent publications have explored the possibility of using fingerprints to confirm drug use, but none has yet dealt with environmental contamination from fingertips. Here we explored the possibility of establishing an environmental cutoff for drug testing from a single fingerprint. METHODS Fingerprint samples (n = 100) were collected from the hands of 50 nondrug users before and after handwashing to establish separate environmental cutoff values and testing protocols for cocaine, benzoylecgonine, heroin, and 6-monoacetylmorphine. The cutoff was challenged by testing the fingerprints of drug-free volunteers after shaking hands with drug users. Fingerprints from patients who testified to taking cocaine (n = 32) and heroin (n = 24) were also collected and analyzed. RESULTS A different cutoff value needed to be applied, depending on whether the fingerprints were collected as presented or after handwashing. Applying these cutoffs gave a 0% false-positive rate from the drug-free volunteers. After application of the cutoff, the detection rate (compared to patient testimony) for washed hands of patients was 87.5% for cocaine use and 100% for heroin use. CONCLUSIONS Fingerprints show enhanced levels of cocaine, heroin, and their respective metabolites in patients who testified to taking the substances, compared with the population of naïve drug users surveyed, and a cutoff (decision level) can be established. The cutoff is robust enough to account for small increases in analyte observed after secondary transfer.

scholarly journals Does the Porter formula hold its promise? A weight estimation formula for macrosomic fetuses put to the test

2019 ◽  
Vol 301 (1) ◽  
pp. 129-135
Author(s):  
Christoph Weiss ◽  
Sabine Enengl ◽  
Simon Hermann Enzelsberger ◽  
Richard Bernhard Mayer ◽  
Peter Oppelt
Keyword(s):  
Clinical Practice ◽  
False Positive ◽  
False Positive Rate ◽  
Normal Weight ◽  
Fetal Weight ◽  
Weight Estimation ◽  
Data Set ◽  
Detection Rates ◽  
Estimation Formula ◽  
Positive Rate

Abstract Purpose Estimating fetal weight using ultrasound measurements is an essential task in obstetrics departments. Most of the commonly used weight estimation formulas underestimate fetal weight when the actual birthweight exceeds 4000 g. Porter et al. published a specially designed formula in an attempt to improve detection rates for such macrosomic infants. In this study, we question the usefulness of the Porter formula in clinical practice and draw attention to some critical issues concerning the derivation of specialized formulas of this type. Methods A retrospective cohort study was carried out, including 4654 singleton pregnancies with a birthweight ≥ 3500 g, with ultrasound examinations performed within 14 days before delivery. Fetal weight estimations derived using the Porter and Hadlock formulas were compared. Results Of the macrosomic infants, 27.08% were identified by the Hadlock formula, with a false-positive rate of 4.60%. All macrosomic fetuses were detected using the Porter formula, with a false-positive rate of 100%; 99.96% of all weight estimations using the Porter formula fell within a range of 4300 g ± 10%. The Porter formula only provides macrosomic estimates. Conclusions The Porter formula does not succeed in distinguishing macrosomic from normal-weight fetuses. High-risk fetuses with a birthweight ≥ 4500 g in particular are not detected more precisely than with the Hadlock formula. For these reasons, we believe that the Porter formula should not be used in clinical practice. Newly derived weight estimation formulas for macrosomic fetuses must not be based solely on a macrosomic data set.

scholarly journals New tools for automated model completion and refinement

2014 ◽  
Vol 70 (a1) ◽  
pp. C327-C327
Author(s):  
Nathaniel Echols ◽  
Nader Morshed ◽  
Nigel Moriarty ◽  
Pavel Afonine ◽  
Thomas Terwilliger ◽  
...  
Keyword(s):  
Model Building ◽  
False Positive Rate ◽  
Molecular Replacement ◽  
Final Model ◽  
Protein Residues ◽  
Manual Intervention ◽  
Positive Rate ◽  
Automated Software ◽  
Model Completion

Although macromolecular crystallography has been greatly accelerated by the development of automated software for data processing, phasing, and model building, most structures require significant manual intervention to yield a truly final model. In addition to missing individual protein or nucleic residues, this may include the addition of alternate conformations, ligands (both free and covalently bound), elemental ions, or modified amino acids. We have developed a number of tools to streamline several of these steps within the Phenix software suite (Adams et al. 2010): 1) an automated pipeline for the determination of ligand-bound structures by molecular replacement (Echols et al. 2014a); 2) placement of elemental ions during refinement (Echols et al. 2014b), as an extension of solvent placement; 3) fitting of additional conformations of protein residues into difference density. These tools reliably reproduce published structures in a majority of test cases, and in several instances identify details omitted by the original authors. Their low false positive rate makes them suitable for use in high-throughput workflows.

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