Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/96754
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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 1474-760X |
Statement of Responsibility: | 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 https://code.google.com/p/methclone. |
Keywords: | Humans Sequence Analysis, DNA Evolution, Molecular DNA Methylation Epigenesis, Genetic Gene Expression Regulation, Leukemic Alleles Software 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 (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
DOI: | 10.1186/s13059-014-0472-5 |
Published version: | http://dx.doi.org/10.1186/s13059-014-0472-5 |
Appears in Collections: | Aurora harvest 3 Medicine publications |
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hdl_96754.pdf | Published version | 1.54 MB | Adobe PDF | View/Open |
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