publication . Article . 2014

Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

Jonathan Z Li; Brad Chapman; Patrick Charlebois; Oliver Hofmann; Brian Weiner; Alyssa J Porter; Reshmi Samuel; Saran Vardhanabhuti; Lu Zheng; Joseph Eron; ...
Open Access English
  • Published: 01 Jan 2014 Journal: PLoS ONE, volume 9, issue 3 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science
  • Country: United States
Abstract
Background The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs. Methods A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naive patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with...
Subjects
free text keywords: Research Article, Biology, Computational Biology, Genomics, Genome Sequencing, Sequence Analysis, Microbiology, Virology, Antivirals, Mathematics, Statistics, Biostatistics, Medicine, Infectious diseases, Viral diseases, HIV, HIV diagnosis and management, Retrovirology and HIV immunopathogenesis, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Illumina dye sequencing, Raltegravir Potassium, Raltegravir, medicine.drug, Integrase inhibitor, Deep sequencing, Pyrosequencing, DNA sequencing
Funded by
NIH| Statistical and Data Management Center for the AIDS Clinical Trials Group
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01AI068634-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| AIDS Clinical Trials Group Network
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01AI068636-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Implications of HIV-1 Minority Variants for Virologic Failure and HIV Reservoirs
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5K08AI100699-04
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Harvard Clinical and Translational Science Center (UL1)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3UL1RR025758-04S1
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
23 references, page 1 of 2

1 Larder BA, Kohli A, Kellam P, Kemp SD, Kronick M, et al (1993) Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing. Nature 365: 671–673.8413632 [OpenAIRE] [PubMed]

2 Church JD, Jones D, Flys T, Hoover D, Marlowe N, et al. (2006) Sensitivity of the ViroSeq HIV-1 genotyping system for detection of the K103N resistance mutation in HIV-1 subtypes A, C, and D. J Mol Diagn 8: : 430-432; quiz 527.

3 Li JZ, Paredes R, Ribaudo HJ, Svarovskaia ES, Metzner KJ, et al (2011) Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis. JAMA 305: 1327–1335.21467286 [OpenAIRE] [PubMed]

4 Boltz VF, Zheng Y, Lockman S, Hong F, Halvas EK, et al (2011) Role of low-frequency HIV-1 variants in failure of nevirapine-containing antiviral therapy in women previously exposed to single-dose nevirapine. Proc Natl Acad Sci U S A 108: 9202–9207.21576473 [OpenAIRE] [PubMed]

5 Karow J (January 19, 2010) Survey: Illumina, SOLiD, and 454 Gain Ground in Research Labs; Most Users Mull Additional Purchases. In Sequence.

6 Department of Health and Human Services. Panel on Antiretroviral Guidelines for Adults and Adolescents. (Feb 12, 2013) Guidelines for the use of antiretroviral agents in HIV-1-in fected adults and adolescents. 1–239.

7 Blanco JL, Varghese V, Rhee SY, Gatell JM, Shafer RW (2011) HIV-1 integrase inhibitor resistance and its clinical implications. J Infect Dis 203: 1204–1214.21459813 [OpenAIRE] [PubMed]

8 Codoner FM, Pou C, Thielen A, Garcia F, Delgado R, et al (2010) Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure. Antiviral Res 88: 281–286.20883724 [PubMed]

9 Charpentier C, Laureillard D, Piketty C, Tisserand P, Batisse D, et al (2010) High frequency of integrase Q148R minority variants in HIV-infected patients naive of integrase inhibitors. AIDS 24: 867–873.20160635 [OpenAIRE] [PubMed]

10 Liu J, Miller MD, Danovich RM, Vandergrift N, Cai F, et al (2011) Analysis of low-frequency mutations associated with drug resistance to raltegravir before antiretroviral treatment. Antimicrob Agents Chemother 55: 1114–1119.21173185 [OpenAIRE] [PubMed]

11 Armenia D, Vandenbroucke I, Fabeni L, Van Marck H, Cento V, et al (2012) Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing. J Infect Dis 205: 557–567.22238474 [OpenAIRE] [PubMed]

12 Taiwo B, Zheng L, Gallien S, Matining RM, Kuritzkes DR, et al (2011) Efficacy of a nucleoside-sparing regimen of darunavir/ritonavir plus raltegravir in treatment-naive HIV-1-infected patients (ACTG A5262). AIDS 25: 2113–2122.21857490 [OpenAIRE] [PubMed]

13 McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303.20644199 [OpenAIRE] [PubMed]

14 Lakhani KR, Boudreau KJ, Loh PR, Backstrom L, Baldwin C, et al (2013) Prize-based contests can provide solutions to computational biology problems. Nat Biotechnol 31: 108–111.23392504 [OpenAIRE] [PubMed]

15 Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, et al (2012) Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol 8: e1002417.22438797 [OpenAIRE] [PubMed]

23 references, page 1 of 2
Abstract
Background The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs. Methods A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naive patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with...
Subjects
free text keywords: Research Article, Biology, Computational Biology, Genomics, Genome Sequencing, Sequence Analysis, Microbiology, Virology, Antivirals, Mathematics, Statistics, Biostatistics, Medicine, Infectious diseases, Viral diseases, HIV, HIV diagnosis and management, Retrovirology and HIV immunopathogenesis, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Illumina dye sequencing, Raltegravir Potassium, Raltegravir, medicine.drug, Integrase inhibitor, Deep sequencing, Pyrosequencing, DNA sequencing
Funded by
NIH| Statistical and Data Management Center for the AIDS Clinical Trials Group
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01AI068634-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| AIDS Clinical Trials Group Network
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01AI068636-03
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Implications of HIV-1 Minority Variants for Virologic Failure and HIV Reservoirs
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5K08AI100699-04
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Harvard Clinical and Translational Science Center (UL1)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3UL1RR025758-04S1
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
23 references, page 1 of 2

1 Larder BA, Kohli A, Kellam P, Kemp SD, Kronick M, et al (1993) Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing. Nature 365: 671–673.8413632 [OpenAIRE] [PubMed]

2 Church JD, Jones D, Flys T, Hoover D, Marlowe N, et al. (2006) Sensitivity of the ViroSeq HIV-1 genotyping system for detection of the K103N resistance mutation in HIV-1 subtypes A, C, and D. J Mol Diagn 8: : 430-432; quiz 527.

3 Li JZ, Paredes R, Ribaudo HJ, Svarovskaia ES, Metzner KJ, et al (2011) Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis. JAMA 305: 1327–1335.21467286 [OpenAIRE] [PubMed]

4 Boltz VF, Zheng Y, Lockman S, Hong F, Halvas EK, et al (2011) Role of low-frequency HIV-1 variants in failure of nevirapine-containing antiviral therapy in women previously exposed to single-dose nevirapine. Proc Natl Acad Sci U S A 108: 9202–9207.21576473 [OpenAIRE] [PubMed]

5 Karow J (January 19, 2010) Survey: Illumina, SOLiD, and 454 Gain Ground in Research Labs; Most Users Mull Additional Purchases. In Sequence.

6 Department of Health and Human Services. Panel on Antiretroviral Guidelines for Adults and Adolescents. (Feb 12, 2013) Guidelines for the use of antiretroviral agents in HIV-1-in fected adults and adolescents. 1–239.

7 Blanco JL, Varghese V, Rhee SY, Gatell JM, Shafer RW (2011) HIV-1 integrase inhibitor resistance and its clinical implications. J Infect Dis 203: 1204–1214.21459813 [OpenAIRE] [PubMed]

8 Codoner FM, Pou C, Thielen A, Garcia F, Delgado R, et al (2010) Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure. Antiviral Res 88: 281–286.20883724 [PubMed]

9 Charpentier C, Laureillard D, Piketty C, Tisserand P, Batisse D, et al (2010) High frequency of integrase Q148R minority variants in HIV-infected patients naive of integrase inhibitors. AIDS 24: 867–873.20160635 [OpenAIRE] [PubMed]

10 Liu J, Miller MD, Danovich RM, Vandergrift N, Cai F, et al (2011) Analysis of low-frequency mutations associated with drug resistance to raltegravir before antiretroviral treatment. Antimicrob Agents Chemother 55: 1114–1119.21173185 [OpenAIRE] [PubMed]

11 Armenia D, Vandenbroucke I, Fabeni L, Van Marck H, Cento V, et al (2012) Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing. J Infect Dis 205: 557–567.22238474 [OpenAIRE] [PubMed]

12 Taiwo B, Zheng L, Gallien S, Matining RM, Kuritzkes DR, et al (2011) Efficacy of a nucleoside-sparing regimen of darunavir/ritonavir plus raltegravir in treatment-naive HIV-1-infected patients (ACTG A5262). AIDS 25: 2113–2122.21857490 [OpenAIRE] [PubMed]

13 McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303.20644199 [OpenAIRE] [PubMed]

14 Lakhani KR, Boudreau KJ, Loh PR, Backstrom L, Baldwin C, et al (2013) Prize-based contests can provide solutions to computational biology problems. Nat Biotechnol 31: 108–111.23392504 [OpenAIRE] [PubMed]

15 Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, et al (2012) Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data. PLoS Comput Biol 8: e1002417.22438797 [OpenAIRE] [PubMed]

23 references, page 1 of 2
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