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Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR

Sam Kint (UGent) , Ward De Spiegelaere (UGent) , Jonas De Kesel (UGent) , Linos Vandekerckhove (UGent) and Wim Van Criekinge (UGent)
(2018) PLOS ONE. 13(6).
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Abstract
DNA methylation is one of the most important epigenetic modifications in the regulation of gene transcription. The current gold standard to study this modification is bisulfite sequencing. Although multiple commercial bisulfite treatment kits provide good conversion efficiencies, DNA loss and especially DNA fragmentation remain troublesome. This hampers DNA methylation profiling of long DNA sequences. Here, we explored the performance of twelve commercial bisulfite kits by an in-depth comparison of DNA fragmentation using gel electrophoresis, qPCR and digital PCR, DNA recovery by spectroscopic measurements and digital PCR and conversion efficiency by next generation sequencing. The results show a clear performance difference between the bisulfite kits, and depending on the specific goal of the study, the most appropriate kit might differ. Moreover, we demonstrated that digital PCR is a valuable method to monitor both DNA fragmentation as well as DNA recovery after bisulfite treatment.
Keywords
PROSTATE-CANCER, CLINICAL VALIDATION, ANTIGEN RECURRENCE, COLORECTAL-CANCER, CPG METHYLATION, DE-NOVO, ASSAY, TRANSCRIPTION, GENOME, HIV-1

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Chicago
Kint, Sam, Ward De Spiegelaere, Jonas De Kesel, Linos Vandekerckhove, and Wim Van Criekinge. 2018. “Evaluation of Bisulfite Kits for DNA Methylation Profiling in Terms of DNA Fragmentation and DNA Recovery Using Digital PCR.” Plos One 13 (6).
APA
Kint, S., De Spiegelaere, W., De Kesel, J., Vandekerckhove, L., & Van Criekinge, W. (2018). Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR. PLOS ONE, 13(6).
Vancouver
1.
Kint S, De Spiegelaere W, De Kesel J, Vandekerckhove L, Van Criekinge W. Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR. PLOS ONE. 2018;13(6).
MLA
Kint, Sam, Ward De Spiegelaere, Jonas De Kesel, et al. “Evaluation of Bisulfite Kits for DNA Methylation Profiling in Terms of DNA Fragmentation and DNA Recovery Using Digital PCR.” PLOS ONE 13.6 (2018): n. pag. Print.
@article{8573869,
  abstract     = {DNA methylation is one of the most important epigenetic modifications in the regulation of gene transcription. The current gold standard to study this modification is bisulfite sequencing. Although multiple commercial bisulfite treatment kits provide good conversion efficiencies, DNA loss and especially DNA fragmentation remain troublesome. This hampers DNA methylation profiling of long DNA sequences. Here, we explored the performance of twelve commercial bisulfite kits by an in-depth comparison of DNA fragmentation using gel electrophoresis, qPCR and digital PCR, DNA recovery by spectroscopic measurements and digital PCR and conversion efficiency by next generation sequencing. The results show a clear performance difference between the bisulfite kits, and depending on the specific goal of the study, the most appropriate kit might differ. Moreover, we demonstrated that digital PCR is a valuable method to monitor both DNA fragmentation as well as DNA recovery after bisulfite treatment.},
  articleno    = {e0199091},
  author       = {Kint, Sam and De Spiegelaere, Ward and De Kesel, Jonas and Vandekerckhove, Linos and Van Criekinge, Wim},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  language     = {eng},
  number       = {6},
  pages        = {17},
  title        = {Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR},
  url          = {http://dx.doi.org/10.1371/journal.pone.0199091},
  volume       = {13},
  year         = {2018},
}

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