Abstract 4529: Tailoring approaches for global epigenome analysis from archival formalin-fixed paraffin-embedded tissue samples
Authors: Das Sudipto , Moran Bruce , Smeets Dominiek , Peuteman Gillian , Klinger Rut , Fender Bozena , Connor Kate , Ebert Matthias , Gaiser Timo , Prehn JHM , Bacon Orna , Kay Elaine , Hennessy Bryan , Murphy Verena , Gallagher William , Byrne Annette , Lambrechts Diether , O’Connor Darran 
Published: July 2016

Abstract
Novel DNA extraction methodologies allow the use of archival material from formalin fixed paraffin embedded (FFPE) tissue samples in genomic studies. A major limitation of this source of DNA is the fragmented nature and low overall yield generally obtained from clinical materials, making downstream applications such as epigenetic analysis challenging. Previous published attempts have focussed on smaller regions of CpG islands, such as the use of Illumina's 450k arrays (which measure methylation at approximately 485,000 sites). The objective of this study was to optimize experimental and analytical workflows that allow effective interrogation of global DNA methylation profiles from FFPE samples.
Methylation capture was conducted on DNA from matched FFPE and fresh frozen samples from the same metastatic colorectal cancer patient as well as two colorectal cancer cell lines, using the SeqCap Epi (Roche) methyl capture system. The custom capture designed includes 5.5 million CpG sites across the genome, a greater than 10-fold increase compared to previously published studies. The wet-lab protocol was robustly optimized for several parameters, such as overall yield and bisulphite conversion efficiency (measured by shallow-read next generation sequencing). A data analysis pipeline composed of the bisulfite-converted DNA aligner BWA-meth, as well as in-house Perl and R scripts, was used to generate detailed methylation maps for individual sample types in order to identify differentially methylated regions (DMRs), which were further validated using targeted bisulphite sequencing for selected loci.
Preliminary analysis of the data revealed 98% bisulphite conversion efficiency and low PCR duplicate rate (4-5%) across both sample types. Intriguingly, we observe an 80% concordance between the overall DNA methylation profiles between FFPE and fresh frozen samples, with a 60% overlap between the FFPE and fresh frozen samples in terms of direction of methylation i.e. hyper or hypomethylation. Mapping overall methylation levels to CpG ‘resorts’ (+/- 4kb of CpG islands) indicated ∼10% of methylation occurred in these regions totalling 245MB. Known genomic features, including exons, promoters of coding/non-coding genes and enhancers, contained ∼30% (1.5 million) of the methylated positions. In addition, this methodology also allowed us to identify C to T transitions across all samples, a common artefact of formalin fixed samples. The analysis revealed that a significantly low proportion of C to T transitions were detected across all samples, the levels of the transitions being consistent between the two sample types. Taken together, these results demonstrate a robust and novel approach to generate DNA methylation profiles from difficult-to-handle, but frequently available material, thus establishing a suitable platform for a whole methylome profiling from archival samples.
Citation Format: Sudipto Das, Bruce Moran, Dominiek Smeets, Gillian Peuteman, Rut Klinger, Bozena Fender, Kate Connor, Matthias Ebert, Timo Gaiser, JHM Prehn, Orna Bacon, Elaine Kay, Bryan Hennessy, Verena Murphy, William Gallagher, Annette Byrne, Diether Lambrechts, Darran O’Connor. Tailoring approaches for global epigenome analysis from archival formalin-fixed paraffin-embedded tissue samples. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4529.