title: A method to evaluate genome-wide methylation in archival formalin-fixed, paraffin-embedded ovarian epithelial cells.
abstract: BACKGROUND
  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. Thus, it is currently not known whether genome-wide methylation can be reliably assessed in DNA from archival FFPE tissue.
  
  
  RESULTS
  Ovarian 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
  We have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples.
authors.affiliation: Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Qiling
authors.initials: Q
authors.lastname: Li
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha, China.
authors.forename: Min
authors.initials: M
authors.lastname: Li
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Li
authors.initials: L
authors.lastname: Ma
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Wenzhi
authors.initials: W
authors.lastname: Li
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha, China.
authors.forename: Xuehong
authors.initials: X
authors.lastname: Wu
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Jendai
authors.initials: J
authors.lastname: Richards
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Guoxing
authors.initials: G
authors.lastname: Fu
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Tameka
authors.initials: T
authors.lastname: Bythwood
authors.affiliation: Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Li
authors.affiliation: School of Information Science and Engineering, Central South University, Changsha, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia, United States of America.
authors.forename: Qing
authors.initials: Q
authors.lastname: Song
mesh_terms: D018899:CpG Islands; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D019175:DNA Methylation; D004847:Epithelial Cells; D005260:Female; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D015894:Genome, Human; D006801:Humans; D010053:Ovary; D016612:Paraffin Embedding; D017422:Sequence Analysis, DNA / Q000379:methods*; D016707:Tissue Fixation
chemical_list: D005404:Fixatives; D005557:Formaldehyde; D004247:DNA