Research Paper Volume 7, Issue 2 pp 97—109
A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data
- 1 Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna 40138, Italy
- 2 Interdepartmental Center “L. Galvani”, University of Bologna, Bologna 40126, Italy
- 3 Personal Genomics S.r.l., Verona 37134, Italy
- 4 Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40126, Italy
- 5 Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Cusano Milanino 20095, Italy
- 6 Department of Physics and Astronomy, University of Bologna, Bologna 40126, Italy
- 7 Institute of Organic Synthesis and Photoreactivity (ISOF) National Research Council (CNR), Bologna 40126, Italy
- 8 Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- 9 Geriatric Unit, IRCCS Ca’ Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
- 10 IRCCS Institute of Neurological Sciences, Bologna, Italy
- 11 Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna 40138, Italy
Received: December 23, 2014 Accepted: January 9, 2015 Published: January 11, 2015
https://doi.org/10.18632/aging.100718How to Cite
Abstract
Aging is characterized by a profound remodeling of the epigenetic architecture in terms of DNA methylation patterns. To date the most effective tool to study genome wide DNA methylation changes is Infinium HumanMethylation450 BeadChip (Infinium 450k). Despite the wealth of tools for Infinium 450k analysis, the identification of the most biologically relevant DNA methylation changes is still challenging. Here we propose an analytical pipeline to select differentially methylated regions (DMRs), tailored on microarray architecture, which is highly effective in highlighting biologically relevant results. The pipeline groups microarray probes on the basis of their localization respect to CpG islands and genic sequences and, depending on probes density, identifies DMRs through a single-probe or a region-centric approach that considers the concomitant variation of multiple adjacent CpG probes. We successfully applied this analytical pipeline on 3 independent Infinium 450k datasets that investigated age-associated changes in blood DNA methylation. We provide a consensus list of genes that systematically vary in DNA methylation levels from 0 to 100 years and that have a potentially relevant role in the aging process.