Disagreement between two common biomarkers of global DNA methylation

  • Background: The quantification of global DNA methylation has been established in epigenetic screening. As more practicable alternatives to the HPLC-based gold standard, the methylation analysis of CpG islands in repeatable elements (LINE-1) and the luminometric methylation assay (LUMA) of overall 5-methylcytosine content in “CCGG” recognition sites are most widely used. Both methods are applied as virtually equivalent, despite the hints that their results only partly agree. This triggered the present agreement assessments. Results: Three different human cell types (cultured MCF7 and SHSY5Y cell lines treated with different chemical modulators of DNA methylation and whole blood drawn from pain patients and healthy volunteers) were submitted to the global DNA methylation assays employing LINE-1 or LUMA-based pyrosequencing measurements. The agreement between the two bioassays was assessed using generally accepted approaches to the statistics for laboratory method comparison studies. Although global DNA methylation levels measured by the two methods correlated, five different lines of statistical evidence consistently rejected the assumption of complete agreement. Specifically, a bias was observed between the two methods. In addition, both the magnitude and direction of bias were tissue-dependent. Interassay differences could be grouped based on Bayesian statistics, and these groups allowed in turn to re-identify the originating tissue. Conclusions: Although providing partly correlated measurements of DNA methylation, interchangeability of the quantitative results obtained with LINE-1 and LUMA was jeopardized by a consistent bias between the results. Moreover, the present analyses strongly indicate a tissue specificity of the differences between the two methods.

Download full text files

Export metadata

Metadaten
Author:Claudia Knothe, Hiromi Shiratori, Eduard Resch, Alfred UltschGND, Gerd GeisslingerORCiDGND, Alexandra Doehring, Jörn LötschORCiDGND
URN:urn:nbn:de:hebis:30:3-441037
DOI:https://doi.org/10.1186/s13148-016-0227-0
ISSN:1868-7083
ISSN:1868-7075
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/27222668
Parent Title (English):Clinical epigenetics
Publisher:BioMed Central
Place of publication:[s. l.]
Document Type:Article
Language:English
Date of Publication (online):2017/05/18
Date of first Publication:2016/05/23
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2017/05/18
Volume:8
Issue:Art. 60
Page Number:17
First Page:1
Last Page:17
Note:
Copyright: © Knothe et al. 2016. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
HeBIS-PPN:427894506
Institutes:Medizin / Medizin
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Sammlungen:Universitätspublikationen
Licence (German):License LogoCreative Commons - Namensnennung 4.0