Title |
Dynamic evolution of clonal epialleles revealed by methclone
|
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Published in |
Genome Biology, September 2014
|
DOI | 10.1186/s13059-014-0472-5 |
Pubmed ID | |
Authors |
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, 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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Norway | 1 | 33% |
United States | 1 | 33% |
Canada | 1 | 33% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 2 | 67% |
Members of the public | 1 | 33% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 5 | 4% |
United Kingdom | 1 | <1% |
New Zealand | 1 | <1% |
Spain | 1 | <1% |
Unknown | 121 | 94% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 46 | 36% |
Researcher | 26 | 20% |
Student > Bachelor | 11 | 9% |
Professor > Associate Professor | 9 | 7% |
Student > Master | 7 | 5% |
Other | 15 | 12% |
Unknown | 15 | 12% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 42 | 33% |
Biochemistry, Genetics and Molecular Biology | 36 | 28% |
Computer Science | 12 | 9% |
Medicine and Dentistry | 9 | 7% |
Mathematics | 3 | 2% |
Other | 10 | 8% |
Unknown | 17 | 13% |