Document Type

Article

Publication Date

1-11-2021

Keywords

JGM, JMG

JAX Source

Sci Rep 2021 Jan 11; 11(1):376

PMID

33432081

DOI

https://doi.org/10.1038/s41598-020-79627-x

Grant

CA034196,GM133562,GM128717

Abstract

Intra-tumoral epigenetic heterogeneity is an indicator of tumor population fitness and is linked to the deregulation of transcription. However, there is no published computational tool to automate the measurement of intra-tumoral epigenetic allelic heterogeneity. We developed an R/Bioconductor package, epihet, to calculate the intra-tumoral epigenetic heterogeneity and to perform differential epigenetic heterogeneity analysis. Furthermore, epihet can implement a biological network analysis workflow for transforming cancer-specific differential epigenetic heterogeneity loci into cancer-related biological function and clinical biomarkers. Finally, we demonstrated epihet utility on acute myeloid leukemia. We found statistically significant differential epigenetic heterogeneity (DEH) loci compared to normal controls and constructed co-epigenetic heterogeneity network and modules. epihet is available at https://bioconductor.org/packages/release/bioc/html/epihet.html .

Comments

The authors thank members of Li Lab for helpful discussions, thank Wojciech Rosikiewicz for figure artistic improvement and thank Stephen Sampson from The Jackson Laboratory Research Program Development for editing this paper. The authors thank The Jackson Laboratory Computational Sciences and Research IT team for technical support and The Jackson Laboratory summer student program.

This article is licensed under a Creative Commons Attribution 4.0 International License.

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