Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F12%3A00383618" target="_blank" >RIV/61388963:_____/12:00383618 - isvavai.cz</a>

Výsledek na webu

<a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049602" target="_blank" >http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049602</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1371/journal.pone.0049602" target="_blank" >10.1371/journal.pone.0049602</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

Popis výsledku v původním jazyce

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

Název v anglickém jazyce

Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

Popis výsledku anglicky

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

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

EE - Mikrobiologie, virologie

OECD FORD obor

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Projekt

<a href="/cs/project/LK11207" target="_blank" >LK11207: Role replikační zdatnosti HIV na průběh nemoci u pacientů bez antiretrovirové léčby</a><br>

Návaznosti

Z - Vyzkumny zamer (s odkazem do CEZ)

Rok uplatnění

2012

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

PLoS ONE

ISSN

1932-6203

e-ISSN

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Svazek periodika

7

Číslo periodika v rámci svazku

11

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

17

Strana od-do

"e49602/1"-"e49602/17"

Kód UT WoS článku

000311151900171

EID výsledku v databázi Scopus

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