In the paper published in the Open Access journal PLoS One, Jaume Roquer and the rest of the authors – all part of the Spanish Stroke Genetics Consortium – used three different commercial kits for DNA extraction for each sample, and then quantified the global DNA methylation (GDM) by a luminometric methylation assay (LUMA). In the 580 samples analysed, they found significant differences in GDM in the same samples between the three DNA isolation methods.
Large epidemiological studies, such as those carried out by the Spanish Stroke Genetics Consortium, are susceptible to accumulate variability by differences in the protocols, sample cohorts, reagent lots, and technologies used. This study demonstrates for the first time that the method of DNA extraction is indeed an important source of variability in LUMA methylation measurements.
The problem of this ‘batch effect’ becomes even more pronounced in collaborative studies, where different cohorts and differences in sample processing may threaten comparability of data and results. That is why the authors – which include Roberto Elosua’s group, also at the IMIM – recommend that methylation studies that apply multiple DNA extraction methods or in cross study comparisons should report the method used, and adjust their methylation results by this variable in order to avoid possible bias, be comparable and reach biologically meaningful conclusions.
Soriano-Tárraga C, Jiménez-Conde J, Giralt-Steinhauer E, Ois A, Rodríguez-Campello A, Cuadrado-Godia E, Fernández-Cadenas I, Montaner J, Lucas G, Elosua R, Roquer J, GeneStroke “The Spanish Stroke Genetics Consortium”. DNA Isolation Method Is a Source of Global DNA Methylation Variability Measured with LUMA. Experimental Analysis and a Systematic Review. PLoS One. 2013;8(4):e60750