Expression and methylation array analysis of CD19+ B-cells from Chronic lymhocytic leukemia (CLL) patients and age matched healthy donor samples [Methylation]

Whole genome sequencing revealed CLL as a disease of the genome and epigenome defined by somatic mutations and aberrant DNA-methylation. To uncover the impact of aberrant methylation on transcription, gene expression and methylation array profiling was performed in CLL and B-cells. DNA from 13 CLL patients and 6 healthy donor samples was analyzed using MCIp-array. Custom made agilent promoter-arrays were used for analysis. Methyl-CpG-Immunoprecipitation (MCIp) was performed with genomic DNA from CD19+ sorted CLL cells and B-cells from chronic lymphocytic leukemia patients and healthy donors, respecitvely. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by density centrifugation using Biocoll. CD19+ PBMCs were purified using CD19 Micro Beads for magnetic positive selection. Genomic DNA was isolated using DNA/RNA allprep Kit (Qiagen) and applied to MCIp. High salt fractions were used for array hybridization.