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

Dumenil, Troy D., Wockner, Leesa F., Bettington, Mark, Mckeone, Diane M., Klein, Kerenaftali, Bowdler, Lisa M., Montgomery, Grant W., Leggett, Barbara A. and Whitehall, Vicki L. J. (2014) Genome-wide DNA methylation analysis of formalin-fixed paraffin embedded colorectal cancer tissue. Genes Chromosomes and Cancer, 53 7: 537-548. doi:10.1002/gcc.22164

Author 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.
Title Genome-wide DNA methylation analysis of formalin-fixed paraffin embedded colorectal cancer tissue
Journal name Genes Chromosomes and Cancer   Check publisher's open access policy
ISSN 1098-2264
Publication date 2014-07
Year available 2014
Sub-type Article (original research)
DOI 10.1002/gcc.22164
Volume 53
Issue 7
Start page 537
End page 548
Total pages 12
Place of publication Hoboken, NJ, United States
Publisher John Wiley & Sons
Collection year 2015
Language eng
Abstract 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.
Keyword Colorectal cancer
Methylation analysis
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Medicine Publications
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