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Cell type-specific signal analysis in EWAS

View ORCID ProfileCharles E. Breeze
doi: https://doi.org/10.1101/2021.05.21.445209
Charles E. Breeze
1Altius Institute for Biomedical Sciences, Seattle, WA, USA 98121
2UCL Cancer Institute, University College London, London WC1E 6BT, UK
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  • ORCID record for Charles E. Breeze
  • For correspondence: c.breeze@ucl.ac.uk
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Abstract

Hundreds of epigenome-wide association studies (EWAS) have been performed, successfully identifying replicated epigenomic signals in processes such as ageing and smoking. Despite this progress, it remains a major challenge in EWAS to detect both cell type-specific and cell type confounding effects impacting study results. One way to identify these effects is through eFORGE (experimentally derived Functional element Overlap analysis of ReGions from EWAS), a published tool that uses 815 datasets from large-scale mapping studies to detect enriched tissues, cell types and genomic regions. Here, I show that eFORGE analysis can be extended to EWAS differentially variable positions (DVPs), identifying target cell types and tissues. In addition, I also show that eFORGE tissue-specific enrichment can be detected for sites below EWAS significance threshold. I develop on these and other analysis examples, extending our knowledge of eFORGE cell type- and tissue-specific enrichment results for different EWAS.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 23, 2021.
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Cell type-specific signal analysis in EWAS
Charles E. Breeze
bioRxiv 2021.05.21.445209; doi: https://doi.org/10.1101/2021.05.21.445209
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Cell type-specific signal analysis in EWAS
Charles E. Breeze
bioRxiv 2021.05.21.445209; doi: https://doi.org/10.1101/2021.05.21.445209

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