title: epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data.
abstract: 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.
authors.affiliation: Department of Mathematical Sciences, University of Copenhagen, Copenhagen, 2100, Denmark.
authors.forename: Martin
authors.initials: M
authors.lastname: Vincent
authors.affiliation: USC Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, 90089-9176, CA, USA.
authors.forename: Kamilla
authors.initials: K
authors.lastname: Mundbjerg
authors.affiliation: Department of Molecular Medicine, Aarhus University Hospital, Aarhus, 8200, Denmark.
authors.forename: Jakob
authors.initials: J
authors.lastname: Skou Pedersen
authors.affiliation: Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, 90089, CA, USA.
authors.forename: Gangning
authors.initials: G
authors.lastname: Liang
authors.affiliation: Van Andel Research Institute, Grand Rapids, 49503, MI, USA.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Jones
authors.affiliation: Department of Molecular Medicine, Aarhus University Hospital, Aarhus, 8200, Denmark.
authors.forename: Torben Falck
authors.initials: TF
authors.lastname: Ørntoft
authors.affiliation: Department of Molecular Medicine, Aarhus University Hospital, Aarhus, 8200, Denmark.
authors.forename: Karina
authors.initials: K
authors.lastname: Dalsgaard Sørensen
authors.affiliation: Department of Mathematical Sciences, University of Copenhagen, Copenhagen, 2100, Denmark. wiuf@math.ku.dk.
authors.forename: Carsten
authors.identifier: 0000-0002-1302-4445
authors.initials: C
authors.lastname: Wiuf
mesh_terms: D000483:Alleles; D018899:CpG Islands; D019175:DNA Methylation; D057890:Epigenomics / Q000379:methods*; D020869:Gene Expression Profiling; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D009707:Nucleosomes / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D009707:Nucleosomes
keywords: CpG methylation; Epi-allele; Epi-allelic haplotype; Epigenetic state; GpC methylation; NOMe-seq