Dynamic evolution of clonal epialleles revealed by methclone
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- 作者：Sheng Li (1) (2)
Francine Garrett-Bakelman (3)
Alexander E Perl (4)
Selina M Luger (4)
Chao Zhang (2) (3)
Bik L To (5)
Ian D Lewis (5) (6)
Anna L Brown (6) (7)
Richard J D鈥橝ndrea (6) (7)
M Elizabeth Ross (8)
Ross Levine (9)
Martin Carroll (4)
Ari Melnick (3)
Christopher E Mason (1) (2) (8)
1. Department of Physiology and Biophysics ; Weill Cornell Medical College ; New York ; NY ; USA
2. The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine ; Weill Cornell Medical College ; New York ; NY ; USA
3. Department of Hematology and Oncology ; Weill Cornell Medical College ; New York ; NY ; USA
4. Division of Hematology and Oncology ; University of Pennsylvania ; Philadelphia ; PA ; USA
5. Directorate of Haematology ; SA Pathology and Department of Haematology ; Royal Adelaide Hospital ; Adelaide ; South Australia
6. Directorate of Haematology and Centre for Cancer Biology SA Pathology ; The Queen Elizabeth Hospital ; Woodville ; South Australia
7. School of Pharmacy and Medical Sciences ; University of South Australia ; Adelaide ; South Australia
8. Feil Family Brain and Mind Research Institute ; Weill Cornell Medical College ; New York ; NY ; USA
9. Memorial Sloan-Kettering Cancer Center ; New York ; NY ; USA - 刊名：Genome Biology
- 出版年：2014
- 出版时间：September 2014
- 年：2014
- 卷：15
- 期：9
- 全文大小：1,473 KB
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- 出版者：BioMed Central
- ISSN：1465-6906
文摘
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.