Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray.
Author(s): Moran S, Vizoso M, Martinez-Cardús A, Gomez A, Matías-Guiu X, Chiavenna SM, Fernandez AG, Esteller M
Publication: Epigenetics, 2014, Vol. 9, Page 829-33
PubMed ID: 24732293 PubMed Review Paper? No
Purpose of Paper
The purpose of this paper was to compare DNA methylation in case-matched OCT-embedded and formalin-fixed paraffin-embedded (FFPE) tumor specimens using an Infinium BeadChip microarray. DNA extracted from FFPE specimens was subjected to a restoration step after bisulfite conversion but prior to analysis.
Conclusion of Paper
Methylation levels for OCT-embedded and FFPE specimens were very strongly correlated. Further, principle component analysis revealed no effect of preservation method and specimens clustered by patient, rather than preservation method, in 24 out of 25 cases. When differences in CpG status were noted between differentially preserved specimens, methylation was found on the OCT-embedded as opposed to the FFPE specimen, which the authors attribute to the inability of the repair method to restore information at the cohesive ends.
Studies
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Study Purpose
The purpose of this study was to compare DNA methylation in case-matched OCT-embedded and FFPE tumor specimens using an Infinium BeadChip microarray. The number of cases examined was as follows: 3 breast tumors, 4 colon tumors, 2 kidney tumors, 5 lung tumors, 4 ovarian tumors, 1 pancreatic tumor, 1 prostate tumor, and 5 stomach tumors. After bisulfate conversion, DNA from FFPE specimens was repaired as described by the Infinium FFPE Restoration guide.
Summary of Findings:
The CpG detection rate for FFPE and OCT-embedded specimens was 99.65% and 99.93%, respectively. Importantly, principle component analysis revealed no effect of preservation method. Methylation levels for frozen and FFPE specimens were very strongly correlated (R2=0.9721). Unsupervised cluster analysis revealed that OCT-embedded and FFPE specimens clustered by patient in 24 out of 25 cases, with the remaining specimen (stomach cancer) clustering within the same tumor type. The number of CpG sites identified as differentially methylated between OCT-embedded and FFPE specimens depended on the differential Beta (β) value threshold, but was generally low (4-311 of 485,512). When differences in CpG status were noted between differentially preserved specimens, methylation was found on the OCT-embedded as opposed to the FFPE specimen, which the authors attribute to the inability of the repair method to restore information at the cohesive ends.
Biospecimens
- Tissue - Breast
- Tissue - Colorectal
- Tissue - Kidney
- Tissue - Stomach
- Tissue - Ovary
- Tissue - Pancreas
- Tissue - Prostate
- Tissue - Lung
Preservative Types
- OCT
- Formalin
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform DNA DNA microarray DNA Bisulfite conversion assay Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
OCT