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eFORGE Project

Project Leader: Charles Breeze

This project involves the development of eFORGE, a computational tool for the analysis of DNA methylation data from Epigenome-Wide Association Studies (EWAS).

eFORGE 450k Analysis

This project focuses on the analysis of data from Illumina's Infinium HumanMethylation450 BeadChip, detecting tissue-specific signal for 450k probe sets. Using the procedure first implemented by the GWAS FORGE project, we currently use data from ENCODE (Thurman et al., 2012) and Epigenomics Roadmap (Stergachis et al., 2013) to generate DHS Hotspot overlap data for all 450k array probes. For each eFORGE analysis we generate random background sets (pairing random probe sets to the input set adjusting for Gene and CpG Island annotation). Comparing DHS Hotspot overlap between input and background probes allows us to test for the tissue-specific enrichment of EWAS probe sets. This tool is designed to aid understanding of disease mechanisms, generating potential new associations with tissues and supporting post-study analysis for EWAS. 

eFORGE 27k Analysis

In a similar way to the 450k analysis we are also focusing on the 27k probes to provide detection of tissue-specific signal for EWAS performed using the Illumina's Infinium HumanMethylation27 BeadChip. 

eFORGE webpage

eFORGE is available from the following webpage (the web interface was developed and is maintained by Javier Herrero at the Bill Lyons Informatics Institute): http://eforge.cs.ucl.ac.uk/ 

Additional documentation on the tool is available on the above eFORGE webpage and in the supplementary GitHub document.

Software Reproducibility

In collaboration with the 2020 Science consortium and the Software Sustainability Institute we are supporting the reproducible development of software, making our software available, comprehensible and annotated. The eFORGE code is available on GitHub, and databases can be downloaded at http://eforge.cs.ucl.ac.uk/?download

References

1. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, et al. The accessible chromatin landscape of the human genome. Nature 2012, 489:75-82.

2. Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, et al. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 2013, 154:888-903.