Statistical methods for classification of 5hmC levels based on the Illumina Inifinium HumanMethylation450 (450k) array data, under the paired bisulfite (BS) and oxidative bisulfite (oxBS) treatment.

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  • Author(s): Slynko A;Slynko A; Benner A; Benner A
  • Source:
    PloS one [PLoS One] 2019 Jun 13; Vol. 14 (6), pp. e0218103. Date of Electronic Publication: 2019 Jun 13 (Print Publication: 2019).
  • Publication Type:
    Journal Article; Research Support, Non-U.S. Gov't
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
    • Publication Information:
      Original Publication: San Francisco, CA : Public Library of Science
    • Subject Terms:
      DNA Methylation*; 5-Methylcytosine/*analogs & derivatives ; Sulfites/*chemistry; 5-Methylcytosine/analysis ; Case-Control Studies ; Humans ; Neoplasms/genetics ; Oxidation-Reduction
    • Abstract:
      Hydroxymethylcytosine (5hmC) methylation is a well-known epigenetic mark that is involved in gene regulation and may impact genome stability. To investigate a possible role of 5hmC in cancer development and progression, one must be able to detect and quantify its level first. In this paper, we address the issue of 5hmC detection at a single base resolution, starting with consideration of the well-established 5hmC measure Δβ and, in particular, with an analysis of its properties, both analytically and empirically. Then we propose several alternative hydroxymethylation measures and compare their properties with those of Δβ. In the absence of a gold standard, the (pairwise) resemblance of those 5hmC measures to Δβ is characterized by means of a similarity analysis and relative accuracy analysis. All results are illustrated on matched healthy and cancer tissue data sets as derived by means of bisulfite (BS) and oxidative bisulfite converting (oxBS) procedures.
      Competing Interests: The authors have declared that no competing interests exist.
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    • Accession Number:
      0 (Sulfites)
      1123-95-1 (5-hydroxymethylcytosine)
      6R795CQT4H (5-Methylcytosine)
      OJ9787WBLU (hydrogen sulfite)
    • Publication Date:
      Date Created: 20190614 Date Completed: 20200214 Latest Revision: 20200309
    • Publication Date:
      20240105
    • Accession Number:
      PMC6563990
    • Accession Number:
      10.1371/journal.pone.0218103
    • Accession Number:
      31194780