title: DNA isolation method is a source of global DNA methylation variability measured with LUMA. Experimental analysis and a systematic review.
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.
authors.affiliation: Neurovascular Research Group. Neurology Department. Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.
authors.forename: Carolina
authors.initials: C
authors.lastname: Soriano-Tárraga
authors.forename: Jordi
authors.initials: J
authors.lastname: Jiménez-Conde
authors.forename: Eva
authors.initials: E
authors.lastname: Giralt-Steinhauer
authors.forename: Angel
authors.initials: A
authors.lastname: Ois
authors.forename: Ana
authors.initials: A
authors.lastname: Rodríguez-Campello
authors.forename: Elisa
authors.initials: E
authors.lastname: Cuadrado-Godia
authors.forename: Israel
authors.initials: I
authors.lastname: Fernández-Cadenas
authors.forename: Joan
authors.initials: J
authors.lastname: Montaner
authors.forename: Gavin
authors.initials: G
authors.lastname: Lucas
authors.forename: Roberto
authors.initials: R
authors.lastname: Elosua
authors.forename: Jaume
authors.initials: J
authors.lastname: Roquer
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D016022:Case-Control Studies; D018899:CpG Islands; D004247:DNA / Q000302:isolation & purification*; D019175:DNA Methylation / Q000235:genetics*; D003920:Diabetes Mellitus / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D005260:Female; D006801:Humans; D006949:Hyperlipidemias / Q000235:genetics / Q000378:metabolism; D006973:Hypertension / Q000235:genetics / Q000378:metabolism; D007963:Leukocytes, Mononuclear / Q000378:metabolism*; D008163:Luminescent Measurements; D008297:Male; D008875:Middle Aged; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D004247:DNA