2 results on '"Turenchalk, Gregory S"'
Number of results to display per page
Search Results
2. A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing
- Author
-
St John, Elizabeth P., Simen, Birgitte B., Turenchalk, Gregory S., Braverman, Michael S., Abbate, Isabella, Aerssens, Jeroen, Bouchez, Olivier, Gabriel, Christian, Izopet, Jacques, Meixenberger, Karolin, Di Giallonardo, Francesca, Schlapbach, Ralph, Paredes, Roger, Sakwa, James, Schmitz-Agheguian, Gudrun G., Thielen, Alexander, Victor, Martin, Metzner, Karin J., Daeumer, Martin P., 454 HIV-1 Alpha Study Group, 454 Life Sciences, Natl Inst Infect Dis L Spallanzani, Janssen Infect Dis Diagnost Bvba, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Blutzentrale Linz, Fac Med Toulouse - U563, Institut National de la Santé et de la Recherche Médicale (INSERM), Robert Koch Institute [Berlin] (RKI), Div Infect Dis & Hosp Epidemiol, University hospital of Zurich [Zurich], Funct Genom Ctr Zurich, University of Zurich, Institut de Recerca de la Sida (IrsiCaixa), Technol Innovat Agcy Natl Genom Platform, Roche Applied Science, Institute of Immunology and Genetics, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), ProdInra, Archive Ouverte, GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Institut National de la Recherche Agronomique ( INRA ), Institut National de la Santé et de la Recherche Médicale ( INSERM ), Robert Koch Institute ( RKI ), and Institut de Recerca de la Sida ( IrsiCaixa )
- Subjects
0301 basic medicine ,[SDV]Life Sciences [q-bio] ,lcsh:Medicine ,population ,Drug resistance ,law.invention ,10234 Clinic for Infectious Diseases ,immunodeficiency-virus ,reverse-transcriptase inhibitor ,minority variant ,low-frequency ,naive patient ,mutation ,protease ,pcr ,diversity ,law ,Amino Acids ,Cooperative Behavior ,lcsh:Science ,Polymerase chain reaction ,education.field_of_study ,Multidisciplinary ,High-Throughput Nucleotide Sequencing ,Amplicon ,3. Good health ,[SDV] Life Sciences [q-bio] ,Plasmids ,Research Article ,Population ,610 Medicine & health ,1100 General Agricultural and Biological Sciences ,Biology ,Tropism ,Deep sequencing ,03 medical and health sciences ,1300 General Biochemistry, Genetics and Molecular Biology ,Drug Resistance, Viral ,Humans ,education ,Genotyping ,1000 Multidisciplinary ,[ SDV ] Life Sciences [q-bio] ,lcsh:R ,Reproducibility of Results ,Molecular biology ,Reverse transcriptase ,030104 developmental biology ,HIV-1 ,lcsh:Q ,Follow-Up Studies - Abstract
Background Ultra deep sequencing is of increasing use not only in research but also in diagnostics. For implementation of ultra deep sequencing assays in clinical laboratories for routine diagnostics, intra- and inter-laboratory testing are of the utmost importance. Methods A multicenter study was conducted to validate an updated assay design for 454 Life Sciences’ GS FLX Titanium system targeting protease/reverse transcriptase (RTP) and env (V3) regions to identify HIV-1 drug-resistance mutations and determine co-receptor use with high sensitivity. The study included 30 HIV-1 subtype B and 6 subtype non-B samples with viral titers (VT) of 3,940–447,400 copies/mL, two dilution series (52,129–1,340 and 25,130–734 copies/mL), and triplicate samples. Amplicons spanning PR codons 10–99, RT codons 1–251 and the entire V3 region were generated using barcoded primers. Analysis was performed using the GS Amplicon Variant Analyzer and geno2pheno for tropism. For comparison, population sequencing was performed using the ViroSeq HIV-1 genotyping system. Results The median sequencing depth across the 11 sites was 1,829 reads per position for RTP (IQR 592–3,488) and 2,410 for V3 (IQR 786–3,695). 10 preselected drug resistant variants were measured across sites and showed high inter-laboratory correlation across all sites with data (P20% were missed, variants 2–10% were detected at most sites (even at low VT), and variants 1–2% were detected by some sites. All mutations detected by population sequencing were also detected by UDS. Conclusions This assay design results in an accurate and reproducible approach to analyze HIV-1 mutant spectra, even at variant frequencies well below those routinely detectable by population sequencing. ISSN:1932-6203
- Published
- 2016
- Full Text
- View/download PDF
Catalog
Books, media, physical & digital resources
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.