Open Access

Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings

  • Authors:
    • Fernando T. Zamuner
    • Ashley Ramos‑lópez
    • Amanda García‑Negrón
    • Ana Purcell‑Wiltz
    • Andrea Cortés‑Ortiz
    • Aniris Román Cuevas
    • Keerthana Gosala
    • Eli Winkler
    • David Sidransky
    • Rafael Guerrero‑Preston
  • View Affiliations

  • Published online on: June 10, 2024     https://doi.org/10.3892/br.2024.1800
  • Article Number: 112
  • Copyright: © Zamuner et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Late‑stage cancers lack effective treatment, underscoring the need for early diagnosis to improve prognosis and decrease mortality rates. Molecular markers, such as DNA methylation, offer promise in early cancer detection. The present study compared commercial kits for analyzing DNA from cervical liquid cytology samples in cancer screening. Rapid bisulfite conversion kits using silica spin‑columns and magnetic beads were assessed against standard DNA extraction and bisulfite conversion methods for profiling DNA methylation using quantitative methylation‑specific PCR. β‑actin amplification indicated the suitability of small sample volumes for methylation studies using either the pellet or supernatant (cell‑free DNA) parts. Comparison of Bisulfite Conversion Kit‑Whole Cell (Abcam), Methylamp Bisulfite Modification (Epigentek), EpiTect Fast LyseAll Bisulfite Kit (Qiagen GmbH) and EZ DNA Methylation‑Direct Kit (Zymo Research Corp.) showed no significant differences in β‑actin cycle threshold values. EZ‑96 DNA Methylation‑Lightning MagPrep (Zymo Research Corp.), a hybrid kit in a 96‑well plate format, exhibited swift turnaround time and similar amplification efficiency. Automation with magnetic bead kits increased throughput without compromising amplification efficiency in open PCR systems. Cost analysis favored direct kits over the gold standard manual protocol. This comparison aids in selecting cost‑effective DNA methylation diagnostic tests. The present study confirmed comparable kit performance in methylation‑based analysis, highlighting the adequacy of cytology samples and the potential of bodily fluids as alternatives for liquid biopsy.

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August-2024
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Spandidos Publications style
Zamuner FT, Ramos‑lópez A, García‑Negrón A, Purcell‑Wiltz A, Cortés‑Ortiz A, Cuevas AR, Gosala K, Winkler E, Sidransky D, Guerrero‑Preston R, Guerrero‑Preston R, et al: Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings. Biomed Rep 21: 112, 2024
APA
Zamuner, F.T., Ramos‑lópez, A., García‑Negrón, A., Purcell‑Wiltz, A., Cortés‑Ortiz, A., Cuevas, A.R. ... Guerrero‑Preston, R. (2024). Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings. Biomedical Reports, 21, 112. https://doi.org/10.3892/br.2024.1800
MLA
Zamuner, F. T., Ramos‑lópez, A., García‑Negrón, A., Purcell‑Wiltz, A., Cortés‑Ortiz, A., Cuevas, A. R., Gosala, K., Winkler, E., Sidransky, D., Guerrero‑Preston, R."Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings". Biomedical Reports 21.2 (2024): 112.
Chicago
Zamuner, F. T., Ramos‑lópez, A., García‑Negrón, A., Purcell‑Wiltz, A., Cortés‑Ortiz, A., Cuevas, A. R., Gosala, K., Winkler, E., Sidransky, D., Guerrero‑Preston, R."Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings". Biomedical Reports 21, no. 2 (2024): 112. https://doi.org/10.3892/br.2024.1800