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Comprehensive Assessment of Concordance Between Fresh-frozen and Formalin-fixed Paraffin Embedded Tumour DNA Methylation using a Targeted Sequencing Approach

ABSTRACT: DNA methylation controls gene expression and is altered in many types of disease, including metastatic colorectal cancer. Studying this phenomenon in archival material such as formalin-fixed paraffin embedded (FFPE) tumour biopsies would represent a significant step in unlocking a previously unavailable source of data. Methylation at base-pair resolution has not been fully described in FFPE samples in the context of matched fresh frozen (FF) tumour material using a targeted next-generation sequencing approach. Here, we used three pairs of matched FFPE and FF samples, along with two cell lines in duplicate, to determine the extent of their similarity. We identified a “bowing” pattern in FFPE samples showing lower CpG proportion at the start of sequence reads, but found no evidence that this significantly affected methylation calls. We also found no significant increase in deamination, measured by C > T transitions, previously considered a result of cross-linking DNA by formalin fixation and a barrier to FFPE use in methylation studies. Finally, our method has shown sensitivity of between 60-70% based on positions also methylated in cell lines. This level is not affected by coverage, and we believe that FFPE material is useful as a tissue source for similar methylation studies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE84171 | GEO | 2017/07/08

SECONDARY ACCESSION(S): PRJNA328217

REPOSITORIES: GEO

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