title: DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.
abstract: To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale.
  
  
  
  Whole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. The findings were confirmed by 450k DNA methylation arrays in a large patient set.
  
  
  
  Compared with mature B or T cells WGBS detected on average 82,000 differentially methylated regions per patient. Differentially methylated regions are enriched to CpG poor regions, active enhancers and transcriptional start sites. We also identified approximately 8000 CpG islands with variable intermediate DNA methylation that seems to occur as a result of stochastic de novo methylation.
  
  
  
  WGBS provides an unbiased view and novel insights into the DNA methylome of ALL cells.
authors.affiliation: Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Per
authors.initials: P
authors.lastname: Wahlberg
authors.affiliation: Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Anders
authors.initials: A
authors.lastname: Lundmark
authors.affiliation: Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Jessica
authors.initials: J
authors.lastname: Nordlund
authors.affiliation: Department of Human Genetics, McGill University & Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
authors.forename: Stephan
authors.initials: S
authors.lastname: Busche
authors.affiliation: Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Amanda
authors.initials: A
authors.lastname: Raine
authors.affiliation: Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden.
authors.forename: Karolina
authors.initials: K
authors.lastname: Tandre
authors.affiliation: Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden.
authors.forename: Lars
authors.initials: L
authors.lastname: Rönnblom
authors.affiliation: Research Center, Sainte-Justine University Health Center; Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada.
authors.forename: Daniel
authors.initials: D
authors.lastname: Sinnett
authors.affiliation: Department of Medical Biosciences, University of Umeå, Umeå, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Forestier
authors.affiliation: Department of Human Genetics, McGill University & Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
authors.forename: Tomi
authors.initials: T
authors.lastname: Pastinen
authors.affiliation: Department of Women's & Children's Health, Pediatric Oncology, Uppsala University, Uppsala, Sweden.
authors.forename: Gudmar
authors.initials: G
authors.lastname: Lönnerholm
authors.affiliation: Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Ann-Christine
authors.initials: AC
authors.lastname: Syvänen
mesh_terms: D002648:Child; D002675:Child, Preschool; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007223:Infant; D008297:Male; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*
keywords: CpG islands; DNA methylation; acute lymphoblastic leukemia; epigenome; methylome; whole-genome bisulfite sequencing