Dynamic evolution of clonal epialleles revealed by methclone

Genome Biol. 2014 Sep 27;15(9):472. doi: 10.1186/s13059-014-0472-5.


We describe methclone, a novel method to identify epigenetic loci that harbor large changes in the clonality of their epialleles (epigenetic alleles). Methclone efficiently analyzes genome-wide DNA methylation sequencing data. We quantify the changes using a composition entropy difference calculation and also introduce a new measure of global clonality shift, loci with epiallele shift per million loci covered, which enables comparisons between different samples to gauge overall epiallelic dynamics. Finally, we demonstrate the utility of methclone in capturing functional epiallele shifts in leukemia patients from diagnosis to relapse. Methclone is open-source and freely available at https://code.google.com/p/methclone.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Evolution, Molecular
  • Gene Expression Regulation, Leukemic
  • Humans
  • Leukemia, Myeloid, Acute / genetics
  • Molecular Sequence Annotation
  • Sequence Analysis, DNA
  • Software*