Recountmethylation enables flexible analysis of public blood DNA methylation array data

Sean K. Maden, Brian Walsh, Kyle Ellrott, Kasper D. Hansen, Reid F. Thompson, Abhinav Nellore

Research output: Contribution to journalArticlepeer-review

Abstract

Summary: Thousands of DNA methylation (DNAm) array samples from human blood are publicly available on the Gene Expression Omnibus (GEO), but they remain underutilized for experiment planning, replication and cross-study and cross-platform analyses. To facilitate these tasks, we augmented our recountmethylation R/Bioconductor package with 12 537 uniformly processed EPIC and HM450K blood samples on GEO as well as several new features. We subsequently used our updated package in several illustrative analyses, finding (i) study ID bias adjustment increased variation explained by biological and demographic variables, (ii) most variation in autosomal DNAm was explained by genetic ancestry and CD4+ T-cell fractions and (iii) the dependence of power to detect differential methylation on sample size was similar for each of peripheral blood mononuclear cells (PBMC), whole blood and umbilical cord blood. Finally, we used PBMC and whole blood to perform independent validations, and we recovered 38-46% of differentially methylated probes between sexes from two previously published epigenome-wide association studies.

Original languageEnglish (US)
Article numbervbad020
JournalBioinformatics Advances
Volume3
Issue number1
DOIs
StatePublished - 2023

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Structural Biology
  • Computer Science Applications

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