Research Papers:

Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach

Bruce Moran, Sudipto Das, Dominiek Smeets, Gillian Peutman, Rut Klinger, Bozena Fender, Kate Connor, Matthias Ebert, Timo Gaiser, Jochen H.M. Prehn, Orna Bacon, Elaine Kay, Bryan Hennessy, Verena Murphy, Bauke Ylstra, Diether Lambrechts, Annette T. Byrne, William M. Gallagher and Darran P. O’Connor _

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Oncotarget. 2017; 8:48126-48137. https://doi.org/10.18632/oncotarget.18296

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Bruce Moran1,10,*, Sudipto Das1,10,*, Dominiek Smeets2,3, Gillian Peutman2,3, Rut Klinger1,10, Bozena Fender4, Kate Connor1,5,10, Matthias Ebert6, Timo Gaiser6, Jochen HM Prehn5, Orna Bacon5,7, Elaine Kay7, Bryan Hennessy7, Verena Murphy8, Bauke Ylstra9, Diether Lambrechts2,3, Annette T. Byrne5, William M. Gallagher4,10,** and Darran P. O’Connor1,10,**

1Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland

2Department of Oncology, Laboratory of Translational Genetics, VIB Center for Cancer Biology, Leuven, Belgium

3Department of Oncology, Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium

4OncoMark Ltd., NovaUCD, Belfield Innovation Park, Dublin, Ireland

5Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland

6Department of Internal Medicine, University of Heidelberg, Mannheim, Germany

7Department of Pathology, Beaumont Hospital, Dublin, Ireland

8Cancer Trials Ireland, Dublin, Ireland

9Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands

10Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College, Dublin, Ireland

*These authors have contributed equally to this work

**Senior co-authors

Correspondence to:

Darran P. O’Connor, email: [email protected]

Keywords: targeted bisulfite sequencing, methylation, epigenetics, FFPE, tumor preservation

Received: July 20, 2016     Accepted: April 03, 2017     Published: May 30, 2017


DNA methylation is altered in many types of disease, including metastatic colorectal cancer. However, the methylome has not yet been fully described in archival formalin-fixed paraffin embedded (FFPE) samples in the context of matched fresh-frozen (FF) tumor material at base-pair resolution using a targeted approach. Using next-generation sequencing, we investigated three pairs of matched FFPE and FF samples to determine the extent of their similarity. We identified a ‘bowing’ pattern specific to FFPE samples categorized by a lower CG proportion at the start of sequence reads. We have found no evidence that this affected methylation calling, nor concordance of results. We also found no significant increase in deamination, measured by C>T transitions, previously considered a result of crosslinking DNA by formalin fixation and a barrier to the use of FFPE in methylation studies. The methods used in this study have shown sensitivity of between 60-70% based on positions also methylated in colorectal cancer cell lines. We demonstrate that FFPE material is a useful source of tumor material for methylation studies using targeted sequencing.

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