Počet záznamů: 1
Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism
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SYSNO ASEP 0383618 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism Tvůrce(i) Archer, J. (GB)
Weber, Jan (UOCHB-X) RID, ORCID
Henry, K. (US)
Winner, D. (US)
Gibson, R. (US)
Lee, L. (US)
Paxinos, E. (US)
Arts, E. J. (US)
Robertson, D. L. (GB)
Mimms, L. (US)
Quinones-Mateu, M. E. (US)Celkový počet autorů 11 Zdroj.dok. PLoS ONE. - : Public Library of Science - ISSN 1932-6203
Roč. 7, č. 11 (2012), e49602/1-e49602/17Poč.str. 17 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova HIV-1 tropism ; V3 region ; deep sequencing Vědní obor RIV EE - Mikrobiologie, virologie CEP LK11207 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy CEZ AV0Z40550506 - UOCHB-X (2005-2011) UT WOS 000311151900171 DOI 10.1371/journal.pone.0049602 Anotace HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile (TM), Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454 (TM) Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454 (TM), PacBio (R) RS (Pacific Biosciences), Illumina (R), and Ion Torrent (TM) (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile (TM) and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage. Pracoviště Ústav organické chemie a biochemie Kontakt asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Rok sběru 2013 Elektronická adresa http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049602
Počet záznamů: 1