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BioMed Research International
Volume 2013 (2013), Article ID 815894, 11 pages
http://dx.doi.org/10.1155/2013/815894
Research Article

Differentially Methylated Loci Distinguish Ovarian Carcinoma Histological Types: Evaluation of a DNA Methylation Assay in FFPE Tissue

1Department of Population Health Research, Alberta Health Services-Cancer Care, Calgary, AB, Canada T2S 3C3
2Departments of Medical Genetics and Oncology, University of Calgary, Calgary, AB, Canada T2N 4N2
3Department of Pathology and Laboratory Medicine, Calgary Laboratory Services, Calgary, AB, Canada T2N 2T9
4Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada T2N 4N2
5Department of Molecular Pathology, Tom Baker Cancer Centre, Alberta Health Services, Calgary, AB, Canada T2N 4N2
6Department of Public Health Sciences, University of Alberta, Edmonton, AB, Canada T6G 1C9

Received 4 July 2013; Accepted 19 August 2013

Academic Editor: John P. Geisler

Copyright © 2013 Linda E. Kelemen et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Epigenomic markers can identify tumor subtypes, but few platforms can accommodate formalin-fixed paraffin-embedded (FFPE) tumor tissue. We tested different amounts of bisulfite-converted (bs) DNA from six FFPE ovarian carcinomas (OC) of serous, endometrioid, and clear cell histologies and two HapMap constitutional genomes to evaluate the performance of the GoldenGate methylation assay. Methylation status at each 1,505 CpG site was expressed as β-values. Comparing 400 ng versus 250 ng bsDNA, reproducibility of the assay ranged from Spearman to 0.90, indicating that β-values obtained with a lower DNA amount did not always correlate well with the higher amount. Average methylation for the six samples was higher using 250 ng (β-value = 0.45, ) than with 400 ng (β-value = 0.36, ). Reproducibility between duplicate HapMap samples ( to 0.92) was also variable. Using 400 ng input bsDNA, THBS2 and ERG were differentially methylated across all histologic types and between endometrioid and clear cell types at <0.1% false discovery rate. Methylation did not always correlate with gene expression ( to 0.15). We found that lower bsDNA overestimates methylation, and, using higher bsDNA amounts, we confirmed a previous report of higher methylation of THBS2 in clear cell OC, which could provide new insight into biological pathways that distinguish OC histological types.