Li 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, Ross M Elizabeth, Levine Ross, Carroll Martin, Melnick Ari, Mason Christopher E
Genome Biol. 2014 Sep 27;15(9):472. doi: 10.1186/s13059-014-0472-5.
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.
我们描述了Methclone，这是一种鉴定表观遗传位点的新方法，这些位点的表观等位基因（epigenetic alleles）的克隆性存在巨大变化。Methclone能有效分析全基因组DNA甲基化测序数据。我们使用成分熵差计算来量化这些变化，还引入了一种新的全局克隆性转移度量方法，即每百万覆盖位点的表观等位基因转移位点，这使得能够在不同样本之间进行比较，以衡量整体表观等位基因动态变化。最后，我们证明了Methclone在捕捉白血病患者从诊断到复发过程中的功能性表观等位基因转移方面的效用。Methclone是开源的，可在https://code.google.com/p/methclone免费获取。
