Premium
Genome‐wide DNA methylation analysis of formalin‐fixed paraffin embedded colorectal cancer tissue
Author(s) -
Dumenil Troy D.,
Wockner Leesa F.,
Bettington Mark,
McKeone Diane M.,
Klein Kerenaftali,
Bowdler Lisa M.,
Montgomery Grant W.,
Leggett Barbara A.,
Whitehall Vicki L.J.
Publication year - 2014
Publication title -
genes, chromosomes and cancer
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.754
H-Index - 119
eISSN - 1098-2264
pISSN - 1045-2257
DOI - 10.1002/gcc.22164
Subject(s) - dna methylation , biology , methylation , microbiology and biotechnology , cpg site , high resolution melt , illumina methylation assay , methylated dna immunoprecipitation , dna , computational biology , genetics , gene , polymerase chain reaction , gene expression
Formalin fixation and embedding of clinical tissue samples in paraffin is a common method for archiving biological material. These samples are often well annotated and provide an invaluable resource for research. However, this process of fixation and storage of tissue leads to DNA damage and fragmentation. The use of DNA from formalin fixed, paraffin‐embedded (FFPE) tissue to interrogate methylation levels on a genome‐wide scale can pose challenges. We compared fresh and matched FFPE tissue DNA samples using the Illumina Infinium HD Human Methylation 450K BeadChip platform with a companion application for repair and “restoration” of DNA from FFPE tissue. Our results showed good correlation between fresh and FFPE sample data. FFPE DNA captured 99% of the CpG sites on the array on average. Significant cancer subgroups based on the CpG island methylator phenotype (CIMP) were clearly distinguished for both fresh and FFPE sample sets with cluster and scaling analysis. The DNA methylation status for the five standard CIMP panel genes which was evaluated for all samples by the MethyLight assay was correctly assigned in both fresh and FFPE samples by the array data. We conclude that the “restoration” method followed by assay on the Infinium HD Human Methylation 450K microarray can produce good quality data for DNA from FFPE samples. © 2014 Wiley Periodicals, Inc.