A Method to Evaluate Genome-Wide Methylation in Archival Formalin-Fixed,Paraffin-Embedded Ovarian Epithelial Cells |
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| Authors: | Qiling Li Min Li Li Ma Wenzhi Li Xuehong Wu Jendai Richards Guoxing Fu Wei Xu Tameka Bythwood Xu Li Jianxin Wang Qing Song |
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| Institution: | 1. Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi''an Jiaotong University, Xi''an, Shaanxi, China.; 2. Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.; 3. School of Information Science and Engineering, Central South University, Changsha, China.; Ohio State University, United States of America, |
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| 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. |
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