Genome‐wide DNA methylation analysis of formalin‐fixed paraffin embedded colorectal cancer tissue

• DOI: 10.1002/gcc.22164
• Publication Date: 2014-03-28T14:09:17Z
• Authors: Troy D. Dumenil; Leesa F. Wockner; Mark Bettington; Diane M. McKeone; Kerenaftali Klein; Lisa M. Bowdler; Grant W. Montgomery; Barbara A. Leggett; Vicki L.J. Whitehall
• Keywords: CpG site; High Resolution Melt; Illumina Methylation Assay; Methylated DNA immunoprecipitation

Formalin fixation and embedding of clinical tissue samples in paraffin is a common method for archiving biological material. These are often well annotated provide an invaluable resource research. However, this process storage leads to DNA damage fragmentation. The use from formalin fixed, paraffin‐embedded (FFPE) interrogate methylation levels on genome‐wide scale can pose challenges. We compared fresh matched FFPE using the Illumina Infinium HD Human Methylation 450K BeadChip platform with companion application repair “restoration” tissue. Our results showed good correlation between sample data. captured 99% CpG sites array average. Significant cancer subgroups based island methylator phenotype (CIMP) were clearly distinguished both sets cluster scaling analysis. status five standard CIMP panel genes which was evaluated all by MethyLight assay correctly assigned conclude that followed microarray produce quality data samples. © 2014 Wiley Periodicals, Inc.