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dc.contributor.author
St John, Elizabeth P.
dc.contributor.author
Simen, Birgitte B.
dc.contributor.author
Turenchalk, Gregory S.
dc.contributor.author
Braverman, Michael S.
dc.contributor.author
Abbate, Isabella
dc.contributor.author
Aerssens, Jeroen
dc.contributor.author
Bouchez, Olivier
dc.contributor.author
Gabriel, Christian
dc.contributor.author
Izopet, Jacques
dc.contributor.author
Meixenberger, Karolin
dc.contributor.author
Di Giallonardo, Francesca
dc.contributor.author
Schlapbach, Ralph
dc.contributor.author
Paredes, Roger
dc.contributor.author
Sakwa, James
dc.contributor.author
Schmitz-Agheguian, Gudrun G.
dc.contributor.author
Thielen, Alexander
dc.contributor.author
Victor, Martin
dc.contributor.author
Metzner, Karin J.
dc.contributor.author
Daeumer, Martin P.
dc.contributor.author
454 HIV-1 Alpha Study Group
dc.date.accessioned
2018-08-16T13:09:45Z
dc.date.available
2018-08-16T13:04:38Z
dc.date.available
2018-08-16T13:09:45Z
dc.date.issued
2016-01-12
dc.identifier.issn
1932-6203
dc.identifier.other
10.1371/journal.pone.0146687
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/112633
dc.identifier.uri
http://hdl.handle.net/20.500.11850/283030
dc.identifier.doi
10.3929/ethz-b-000112633
dc.description.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 (P<0.001). The triplicate samples of a plasmid mixture confirmed the high inter-laboratory consistency (mean% ± stdev: 4.6 ±0.5, 4.8 ±0.4, 4.9 ±0.3) and revealed good intra-laboratory consistency (mean% range ± stdev range: 4.2–5.2 ± 0.04–0.65). In the two dilutions series, no variants >20% 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.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Public Library of Science (PLoS)
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.title
A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
ethz.journal.title
PLoS ONE
ethz.journal.volume
11
en_US
ethz.journal.issue
1
en_US
ethz.journal.abbreviated
PLoS ONE
ethz.pages.start
e0146687
en_US
ethz.size
17 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.identifier.nebis
006206116
ethz.publication.place
San Francisco, CA
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00003 - Schulleitung und Dienste::00022 - Bereich VP Forschung & Wirtschaftsbez. / Domain VP Research & Corporate Relations::02207 - Functional Genomics Center Zürich / Functional Genomics Center Zürich
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02030 - Dep. Biologie / Dep. of Biology::08828 - Schlapbach, Ralph (Tit.-Prof.)
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00003 - Schulleitung und Dienste::00022 - Bereich VP Forschung & Wirtschaftsbez. / Domain VP Research & Corporate Relations::02207 - Functional Genomics Center Zürich / Functional Genomics Center Zürich
ethz.date.deposited
2017-06-12T00:21:34Z
ethz.source
ECIT
ethz.identifier.importid
imp593654173806b84543
ethz.ecitpid
pub:174220
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2018-08-16T13:04:42Z
ethz.rosetta.lastUpdated
2018-11-07T23:27:04Z
ethz.rosetta.versionExported
true
dc.identifier.olduri
http://hdl.handle.net/20.500.11850/164470
dc.identifier.olduri
http://hdl.handle.net/20.500.11850/112633
ethz.COinS
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