TitleDynamic evolution of clonal epialleles revealed by methclone.
Publication TypeJournal Article
Year of Publication2014
AuthorsLi, Sheng, Garrett-Bakelman Francine, Perl Alexander E., Luger Selina M., Zhang Chao, To Bik L., Lewis Ian D., Brown Anna L., D'Andrea Richard J., M Ross Elizabeth, Levine Ross, Carroll Martin, Melnick Ari, and Mason Christopher E.
JournalGenome Biol
Volume15
Issue9
Pagination472
Date Published2014 Sep 27
ISSN1474-760X
KeywordsAlleles, DNA Methylation, Epigenesis, Genetic, Evolution, Molecular, Gene Expression Regulation, Leukemic, Humans, Leukemia, Myeloid, Acute, Molecular Sequence Annotation, Sequence Analysis, DNA, Software
Abstract

<p>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.</p>

DOI10.1186/s13059-014-0472-5
Alternate JournalGenome Biol
PubMed ID25260792
PubMed Central IDPMC4242486
Grant ListR01 CA198089 / CA / NCI NIH HHS / United States
K08 CA169055 / CA / NCI NIH HHS / United States
R01CA149566 / CA / NCI NIH HHS / United States
R01 CA149566 / CA / NCI NIH HHS / United States
R01HG006798 / HG / NHGRI NIH HHS / United States
R01 HG006798 / HG / NHGRI NIH HHS / United States
R01 NS076465 / NS / NINDS NIH HHS / United States
K08CA169055 / CA / NCI NIH HHS / United States
R01NS076465 / NS / NINDS NIH HHS / United States