Introduction

The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We develop a statistical method, epiG, to infer and differentiate between different epi-allelic haplotypes, annotated with CpG methylation status and DNA polymorphisms, from whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq data. We demonstrate the capabilities of the method by inferring allele-specific methylation and nucleosome occupancy in cell lines, and colon and tumor samples, and by benchmarking the method against independent experimental data.

Publications

  1. epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data.
    Cite this
    Vincent M, Mundbjerg K, Skou Pedersen J, Liang G, Jones PA, Ørntoft TF, Dalsgaard Sørensen K, Wiuf C, 2017-02-01 - Genome biology

Credits

  1. Martin Vincent
    Developer

    Department of Mathematical Sciences, University of Copenhagen, Denmark

  2. Kamilla Mundbjerg
    Developer

    USC Norris Comprehensive Cancer Center, Keck School of Medicine, United States of America

  3. Jakob Skou Pedersen
    Developer

    Department of Molecular Medicine, Aarhus University Hospital, Denmark

  4. Gangning Liang
    Developer

    Department of Urology, Keck School of Medicine, United States of America

  5. Peter A Jones
    Developer

    Van Andel Research Institute, Grand Rapids, United States of America

  6. Torben Falck Ørntoft
    Developer

    Department of Molecular Medicine, Aarhus University Hospital, Denmark

  7. Karina Dalsgaard Sørensen
    Developer

    Department of Molecular Medicine, Aarhus University Hospital, Denmark

  8. Carsten Wiuf
    Investigator

    Department of Mathematical Sciences, University of Copenhagen, Denmark

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Summary
AccessionBT005092
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++, R
User InterfaceTerminal Command Line
Download Count0
Country/RegionDenmark
Submitted ByCarsten Wiuf