ArticlePloS one2014
A method to evaluate genome-wide methylation in archival formalin-fixed, paraffin-embedded ovarian epithelial cells.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer.Molecular oncology · 2021Article
- Aberrant expression and high-frequency mutations ofExperimental and therapeutic medicine · 2019Article
- Klotho inhibits EGF-induced cell migration in Caki-1 cells through inactivation of EGFR and p38 MAPK signaling pathways.Oncotarget · 2018Article
- A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA.BMC medical genomics · 2017Article
- Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach.Oncotarget · 2017Article
- Tumour heterogeneity: principles and practical consequences.Virchows Archiv : an international journal of pathology · 2016Review
- Article
- References for Haplotype Imputation in the Big Data Era.Molecular biology (Los Angeles, Calif.) · 2015Article
- The mirror RNA expression pattern in human tissues.Precision medicine · 2015Article
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Authors and funding
12 authors.
Funding
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/SIGNIFICANCE: We have developed an efficient method that allows DNA methylation to be assessed in archival FFPE tissue samples.
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