Abstract
BackgroundThe use of DNA from archival formalin and paraffin embedded (FFPE) tissue for genetic and epigenetic analyses may be problematic, since the DNA is often degraded and only limited amounts may be available. Thus, it is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue.Methodology/Principal FindingsOvarian tissues, which were obtained and formalin-fixed and paraffin-embedded in either 1999 or 2011, were sectioned and stained with hematoxylin-eosin (H&E).Epithelial cells were captured by laser micro dissection, and their DNA subjected to whole genomic bisulfite conversion, whole genomic polymerase chain reaction (PCR) amplification, and purification. Sequencing and software analyses were performed to identify the extent of genomic methylation. We observed that 31.7% of sequence reads from the DNA in the 1999 archival FFPE tissue, and 70.6% of the reads from the 2011 sample, could be matched with the genome. Methylation rates of CpG on the Watson and Crick strands were 32.2% and 45.5%, respectively, in the 1999 sample, and 65.1% and 42.7% in the 2011 sample.Conclusions/SignificanceWe have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples.
Highlights
Epigenetics is the study of heritable changes in gene expression that are not attributable to alterations in the DNA sequence
Conclusions/Significance: We have developed an efficient method that allows DNA methylation to be assessed in archival from archival formalin and paraffin embedded (FFPE) tissue samples
With recently developed technology in the field of genetics and epigenetics, some investigators are working to refine capture protocols to reduce sample input requirements and enhance multiplexing capabilities, while others intend to refine detection to single-cell and even single-molecule resolution [2,8]. This developing technology provides us with an opportunity to assess changes in genome-wide DNA methylation in FFPE tissues that have been stored for a long time
Summary
Epigenetics is the study of heritable changes in gene expression that are not attributable to alterations in the DNA sequence. With the increasing interest in understanding the genetic and epigenetic basis of diseases, the ability to extract DNA from these FFPE samples represents an invaluable source of diagnostic material that can be used for genomic analyses and translational studies. The use of DNA from archival formalin and paraffin embedded (FFPE) tissue for genetic and epigenetic analyses may be problematic, since the DNA is often degraded and only limited amounts may be available. It is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue
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