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In-depth validation of total HIV-1 DNA assays for quantification of various HIV-1 subtypes

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Abstract
HIV-1 DNA quantification serves as an important reservoir biomarker in HIV cure trials. However, the high genetic diversity of HIV-1 represented by different subtypes may bring inaccuracy in quantifying HIV-1 DNA and a sensitive and validated assay covering diverse HIV-1 subtypes is lacking. Therefore, we cross-validated total HIV-1 DNA assays described in literature using a three-step comparative analysis. First, a bioinformatics tool was developed in-house to perform an in silico evaluation of 67 HIV-1 DNA assays. Secondly, these selected assays were in vitro validated using a panel of different HIV-1 subtypes and, finally, ex vivo assessed on selected patient samples with different HIV-1 subtypes. Our results show that quantification of HIV-1 DNA substantially differs between assays and we advise five best performing HIV-1 DNA assays for ddPCR and qPCR (Schvachsa_2007, Viard_2004, Heeregrave_2009, Van_der_Sluis_2013, Yu_2008 and Yun_2002). This in-depth analysis of published HIV-1 DNA assays indicates that not all assays guarantee an optimal measurement of HIV-1 DNA, especially when looking across subtypes. Using an in-depth cross-validation, we were able to validate HIV-1 DNA assays that are suitable for quantification of HIV-1 DNA in a wide variety of HIV-1 infected patients.
Keywords
REAL-TIME PCR, DROPLET-DIGITAL PCR, PROVIRAL LOAD, QUANTITATION, CELLS, ASSOCIATION, DIAGNOSIS, RNA

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MLA
Rutsaert, Sofie, Ward De Spiegelaere, Clarissa Van Hecke, et al. “In-depth Validation of Total HIV-1 DNA Assays for Quantification of Various HIV-1 Subtypes.” SCIENTIFIC REPORTS 8 (2018): n. pag. Print.
APA
Rutsaert, S., De Spiegelaere, W., Van Hecke, C., De Scheerder, M.-A., Kiselinova, M., Vervisch, K., Trypsteen, W., et al. (2018). In-depth validation of total HIV-1 DNA assays for quantification of various HIV-1 subtypes. SCIENTIFIC REPORTS, 8.
Chicago author-date
Rutsaert, Sofie, Ward De Spiegelaere, Clarissa Van Hecke, Marie-Angélique De Scheerder, Maja Kiselinova, Karen Vervisch, Wim Trypsteen, and Linos Vandekerckhove. 2018. “In-depth Validation of Total HIV-1 DNA Assays for Quantification of Various HIV-1 Subtypes.” Scientific Reports 8.
Chicago author-date (all authors)
Rutsaert, Sofie, Ward De Spiegelaere, Clarissa Van Hecke, Marie-Angélique De Scheerder, Maja Kiselinova, Karen Vervisch, Wim Trypsteen, and Linos Vandekerckhove. 2018. “In-depth Validation of Total HIV-1 DNA Assays for Quantification of Various HIV-1 Subtypes.” Scientific Reports 8.
Vancouver
1.
Rutsaert S, De Spiegelaere W, Van Hecke C, De Scheerder M-A, Kiselinova M, Vervisch K, et al. In-depth validation of total HIV-1 DNA assays for quantification of various HIV-1 subtypes. SCIENTIFIC REPORTS. 2018;8.
IEEE
[1]
S. Rutsaert et al., “In-depth validation of total HIV-1 DNA assays for quantification of various HIV-1 subtypes,” SCIENTIFIC REPORTS, vol. 8, 2018.
@article{8582760,
  abstract     = {HIV-1 DNA quantification serves as an important reservoir biomarker in HIV cure trials. However, the high genetic diversity of HIV-1 represented by different subtypes may bring inaccuracy in quantifying HIV-1 DNA and a sensitive and validated assay covering diverse HIV-1 subtypes is lacking. Therefore, we cross-validated total HIV-1 DNA assays described in literature using a three-step comparative analysis. First, a bioinformatics tool was developed in-house to perform an in silico evaluation of 67 HIV-1 DNA assays. Secondly, these selected assays were in vitro validated using a panel of different HIV-1 subtypes and, finally, ex vivo assessed on selected patient samples with different HIV-1 subtypes. Our results show that quantification of HIV-1 DNA substantially differs between assays and we advise five best performing HIV-1 DNA assays for ddPCR and qPCR (Schvachsa_2007, Viard_2004, Heeregrave_2009, Van_der_Sluis_2013, Yu_2008 and Yun_2002). This in-depth analysis of published HIV-1 DNA assays indicates that not all assays guarantee an optimal measurement of HIV-1 DNA, especially when looking across subtypes. Using an in-depth cross-validation, we were able to validate HIV-1 DNA assays that are suitable for quantification of HIV-1 DNA in a wide variety of HIV-1 infected patients.},
  articleno    = {17274},
  author       = {Rutsaert, Sofie and De Spiegelaere, Ward and Van Hecke, Clarissa and De Scheerder, Marie-Angélique and Kiselinova, Maja and Vervisch, Karen and Trypsteen, Wim and Vandekerckhove, Linos},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keywords     = {REAL-TIME PCR,DROPLET-DIGITAL PCR,PROVIRAL LOAD,QUANTITATION,CELLS,ASSOCIATION,DIAGNOSIS,RNA},
  language     = {eng},
  pages        = {8},
  title        = {In-depth validation of total HIV-1 DNA assays for quantification of various HIV-1 subtypes},
  url          = {http://dx.doi.org/10.1038/s41598-018-35403-6},
  volume       = {8},
  year         = {2018},
}

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