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Type: Journal article
Title: Dynamic evolution of clonal epialleles revealed by methclone
Author: Li, S.
Garrett-Bakelman, F.
Perl, A.
Luger, S.
Zhang, C.
To, B.
Lewis, I.
Brown, A.
D'Andrea, R.
Ross, M.
Levine, R.
Carroll, M.
Melnick, A.
Mason, C.
Citation: Genome Biology, 2014; 15(9):472-1-472-12
Publisher: BioMed Central
Issue Date: 2014
ISSN: 1474-760X
Statement of
Sheng Li, Francine Garrett-Bakelman, Alexander E Perl, Selina M Luger, Chao Zhang, Bik L To, Ian D Lewis, Anna L Brown, Richard J D’Andrea, M Elizabeth Ross, Ross Levine, Martin Carroll, Ari Melnick, and Christopher E Mason
Abstract: 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
Keywords: Humans
Sequence Analysis, DNA
Evolution, Molecular
DNA Methylation
Epigenesis, Genetic
Gene Expression Regulation, Leukemic
Leukemia, Myeloid, Acute
Molecular Sequence Annotation
Rights: © 2014 Li et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
DOI: 10.1186/s13059-014-0472-5
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