schliessen

Filtern

 

Bibliotheken

Low-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance (Ultra-Wide HIV Drug Resistance Genotyping)

Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures th... Full description

Journal Title: PLoS ONE 2012, Vol.7(5), p.e36494
Main Author: Dudley, Dawn M
Other Authors: Chin, Emily N , Bimber, Benjamin N , Sanabani, Sabri S , Tarosso, Leandro F , Costa, Priscilla R , Sauer, Mariana M , Kallas, Esper G , O.’Connor, David H
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0036494
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: plos10.1371/journal.pone.0036494
title: Low-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance (Ultra-Wide HIV Drug Resistance Genotyping)
format: Article
creator:
  • Dudley, Dawn M
  • Chin, Emily N
  • Bimber, Benjamin N
  • Sanabani, Sabri S
  • Tarosso, Leandro F
  • Costa, Priscilla R
  • Sauer, Mariana M
  • Kallas, Esper G
  • O.’Connor, David H
subjects:
  • Research Article
  • Biology
  • Medicine
  • Virology
  • Infectious Diseases
  • Computational Biology
ispartof: PLoS ONE, 2012, Vol.7(5), p.e36494
description: Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. ; We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in São Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naïve individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. ; The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3–5× less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.
language: eng
source:
identifier: E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0036494
fulltext: fulltext
issn:
  • 1932-6203
  • 19326203
url: Link


@attributes
ID1857431609
RANK0.07
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
LOCALfalse
PrimoNMBib
record
control
sourcerecordid10.1371/journal.pone.0036494
sourceidplos
recordidTN_plos10.1371/journal.pone.0036494
sourcesystemOther
pqid1324609865
display
typearticle
titleLow-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance (Ultra-Wide HIV Drug Resistance Genotyping)
creatorDudley, Dawn M ; Chin, Emily N ; Bimber, Benjamin N ; Sanabani, Sabri S ; Tarosso, Leandro F ; Costa, Priscilla R ; Sauer, Mariana M ; Kallas, Esper G ; O.’Connor, David H
contributorBarbour, Jason D. (Editor)
ispartofPLoS ONE, 2012, Vol.7(5), p.e36494
identifierE-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0036494
subjectResearch Article ; Biology ; Medicine ; Virology ; Infectious Diseases ; Computational Biology
descriptionGreat efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. ; We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in São Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naïve individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. ; The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3–5× less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.
languageeng
source
version8
lds50peer_reviewed
links
openurl$$Topenurl_article
openurlfulltext$$Topenurlfull_article
search
creatorcontrib
0Dudley, Dawn M
1Chin, Emily N
2Bimber, Benjamin N
3Sanabani, Sabri S
4Tarosso, Leandro F
5Costa, Priscilla R
6Sauer, Mariana M
7Kallas, Esper G
8O.’Connor, David H
9Barbour, Jason D. (Editor)
titleLow-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance (Ultra-Wide HIV Drug Resistance Genotyping)
descriptionGreat efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. ; We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in São Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naïve individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. ; The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3–5× less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.
subject
0Research Article
1Biology
2Medicine
3Virology
4Infectious Diseases
5Computational Biology
general
010.1371/journal.pone.0036494
1English
sourceidplos
recordidplos10.1371/journal.pone.0036494
issn
01932-6203
119326203
rsrctypearticle
creationdate2012
recordtypearticle
addtitle
0PLoS ONE
1Ultra-Wide HIV Drug Resistance Genotyping
searchscopeplos
scopeplos
lsr30VSR-Enriched:[pqid]
sort
titleLow-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance (Ultra-Wide HIV Drug Resistance Genotyping)
authorDudley, Dawn M ; Chin, Emily N ; Bimber, Benjamin N ; Sanabani, Sabri S ; Tarosso, Leandro F ; Costa, Priscilla R ; Sauer, Mariana M ; Kallas, Esper G ; O.’Connor, David H
creationdate20120504
facets
frbrgroupid7177480164965828409
frbrtype5
languageeng
creationdate2012
topic
0Research Article
1Biology
2Medicine
3Virology
4Infectious Diseases
5Computational Biology
collectionPLoS
prefilterarticles
rsrctypearticles
creatorcontrib
0Dudley, Dawn M
1Chin, Emily N
2Bimber, Benjamin N
3Sanabani, Sabri S
4Tarosso, Leandro F
5Costa, Priscilla R
6Sauer, Mariana M
7Kallas, Esper G
8O.’Connor, David H
9Barbour, Jason D.
jtitlePLoS ONE
toplevelpeer_reviewed
frbr
t2
k12012
k219326203
k310.1371/journal.pone.0036494
k47
k55
k636494
k7plos one
k8low cost ultra wide genotyping using roche 454 pyrosequencing for surveillance of hiv drug resistance
k9lowcostultrawidegenotance
k12lowcostultrawidegenotypin
k15dawnmdudley
k16dudleydawnm
delivery
delcategoryRemote Search Resource
fulltextfulltext
ranking
booster11
booster21
pcg_typepublisher
addata
aulast
0Dudley
1Chin
2Bimber
3Sanabani
4Tarosso
5Costa
6Sauer
7Kallas
8O.’Connor
9Barbour
aufirst
0Dawn M.
1Emily N.
2Benjamin N.
3Sabri S.
4Leandro F.
5Priscilla R.
6Mariana M.
7Esper G.
8David H.
9Jason D.
au
0Dudley, Dawn M
1Chin, Emily N
2Bimber, Benjamin N
3Sanabani, Sabri S
4Tarosso, Leandro F
5Costa, Priscilla R
6Sauer, Mariana M
7Kallas, Esper G
8O.’Connor, David H
addauBarbour, Jason D.
atitleLow-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance (Ultra-Wide HIV Drug Resistance Genotyping)
jtitlePLoS ONE
risdate20120504
volume7
issue5
spagee36494
pagese36494
eissn1932-6203
genrearticle
ristypeJOUR
abstractGreat efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. ; We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in São Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naïve individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. ; The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3–5× less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.
copSan Francisco, USA
pubPublic Library of Science
doi10.1371/journal.pone.0036494
oafree_for_read
date2012-05-04