DNA Isolation Method Is a Source of Global DNA Methylation Variability Measured with LUMA. Experimental Analysis and a Systematic Review

Carolina Soriano-Tárraga, Jordi Jiménez-Conde, Eva Giralt-Steinhauer, Ángel Ois, Ana Rodríguez-Campello, Elisa Cuadrado-Godia, Israel Fernández-Cadenas, Joan Montaner, Gavin Lucas, Roberto Elosua, Jaume Roquer

Research output: Contribution to journalReview article

16 Scopus citations

Abstract

In DNA methylation, methyl groups are covalently bound to CpG dinucleotides. However, the assumption that methyl groups are not lost during routine DNA extraction has not been empirically tested. To avoid nonbiological associations in DNA methylation studies, it is essential to account for potential batch effect bias in the assessment of this epigenetic mechanism. Our purpose was to determine if the DNA isolation method is an independent source of variability in methylation status. We quantified Global DNA Methylation (GDM) by luminometric methylation assay (LUMA), comparing the results from 3 different DNA isolation methods. In the controlled analysis (n = 9), GDM differed slightly for the same individual depending on extraction method. In the population analysis (n = 580) there were significant differences in GDM between the 3 DNA isolation methods (medians, 78.1%, 76.5% and 75.1%; p<0.001). A systematic review of published data from LUMA GDM studies that specify DNA extraction methods is concordant with our findings. DNA isolation method is a source of GDM variability measured with LUMA. To avoid possible bias, the method used should be reported and taken into account in future DNA methylation studies.

Original languageEnglish
Article numbere60750
JournalPloS one
Volume8
Issue number4
DOIs
StatePublished - Apr 9 2013
Externally publishedYes

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    Soriano-Tárraga, C., Jiménez-Conde, J., Giralt-Steinhauer, E., Ois, Á., Rodríguez-Campello, A., Cuadrado-Godia, E., Fernández-Cadenas, I., Montaner, J., Lucas, G., Elosua, R., & Roquer, J. (2013). DNA Isolation Method Is a Source of Global DNA Methylation Variability Measured with LUMA. Experimental Analysis and a Systematic Review. PloS one, 8(4), [e60750]. https://doi.org/10.1371/journal.pone.0060750