A meta-analysis on age-associated changes in blood DNA methylation: Results from an original analysis pipeline for Infinium 450k data

Maria Giulia Bacalini, Alessio Boattini, Davide Gentilini, Enrico Giampieri, Chiara Pirazzini, Cristina Giuliani, Elisa Fontanesi, Daniel Remondini, Miriam Capri, Alberto Del Rio, Donata Luiselli, Giovanni Vitale, Daniela Mari, Gastone Castellani, Anna Maria Di Blasio, Stefano Salvioli, Claudio Franceschi, Paolo Garagnani

Research output: Contribution to journalArticle

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 regioncentric 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.

Original languageEnglish
Pages (from-to)97-109
Number of pages13
JournalAging
Volume7
Issue number2
Publication statusPublished - 2015

Keywords

  • Aging
  • DNA methylation
  • Epigenetics
  • Infinium human methylation 450 beadchip

ASJC Scopus subject areas

  • Ageing
  • Cell Biology

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    Bacalini, M. G., Boattini, A., Gentilini, D., Giampieri, E., Pirazzini, C., Giuliani, C., Fontanesi, E., Remondini, D., Capri, M., Rio, A. D., Luiselli, D., Vitale, G., Mari, D., Castellani, G., Di Blasio, A. M., Salvioli, S., Franceschi, C., & Garagnani, P. (2015). A meta-analysis on age-associated changes in blood DNA methylation: Results from an original analysis pipeline for Infinium 450k data. Aging, 7(2), 97-109.