Per Wahlberg1, Anders Lundmark1, Jessica Nordlund1, Stephan Busche2, Amanda Raine1, Karolina Tandre3, Lars Rönnblom3, Daniel Sinnett4, Erik Forestier5, Tomi Pastinen2, Gudmar Lönnerholm6, Ann-Christine Syvänen1. 1. Department of Medical Sciences, Molecular Medicine & Science for Life Laboratory, Uppsala University, Uppsala, Sweden. 2. Department of Human Genetics, McGill University & Genome Quebec Innovation Centre, Montreal, Quebec, Canada. 3. Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden. 4. Research Center, Sainte-Justine University Health Center; Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada. 5. Department of Medical Biosciences, University of Umeå, Umeå, Sweden. 6. Department of Women's & Children's Health, Pediatric Oncology, Uppsala University, Uppsala, Sweden.
Abstract
AIM: To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. MATERIALS & METHODS: 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. RESULTS: 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. CONCLUSION: WGBS provides an unbiased view and novel insights into the DNA methylome of ALL cells.
AIM: To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. MATERIALS & METHODS: 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. RESULTS: 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. CONCLUSION: WGBS provides an unbiased view and novel insights into the DNA methylome of ALL cells.
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