Abstract
Background and MethodsFormalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. Recently, the Whole Genome (WG) DASL (cDNA-mediated Annealing, Selection, extension and Ligation) assay was specifically developed to profile FFPE tissue. However, a thorough comparison of data generated from FFPE RNA and Fresh Frozen (FF) RNA using this platform is lacking. To this end we profiled, in duplicate, 20 FFPE tissues and 20 matched FF tissues and evaluated the concordance of the DASL results from FFPE and matched FF material.Methodology and Principal FindingsWe show that after proper normalization, all FFPE and FF pairs exhibit a high level of similarity (Pearson correlation >0.7), significantly larger than the similarity between non-paired samples. Interestingly, the probes showing the highest correlation had a higher percentage G/C content and were enriched for cell cycle genes. Predictions of gene expression signatures developed on frozen material (Intrinsic subtype, Genomic Grade Index, 70 gene signature) showed a high level of concordance between FFPE and FF matched pairs. Interestingly, predictions based on a 60 gene DASL list (best match with the 70 gene signature) showed very high concordance with the MammaPrint® results.Conclusions and SignificanceWe demonstrate that data generated from FFPE material with the DASL assay, if properly processed, are comparable to data extracted from the FF counterpart. Specifically, gene expression profiles for a known set of prognostic genes for a specific disease are highly comparable between two conditions. This opens up the possibility of using both FFPE and FF material in gene expressions analyses, leading to a vast increase in the potential resources available for cancer research.
Highlights
Tissue samples collected during surgery as well as biopsies are often fixed in Formalin and embedded in Paraffin (FFPE).Molecular genomics assays on archived Formalin Fixed Paraffin Embedded (FFPE) blocks, together with clinicopathological information, can provide critical insights into a heterogeneous disease like breast cancer, especially considering the fact that FFPE samples are the most widely available source of tissue material for which long-term clinical follow-up data are recorded
We demonstrate that data generated from FFPE material with the DASL assay, if properly processed, are comparable to data extracted from the Fresh Frozen (FF) counterpart
DASL with the specific aim of overcoming the technical limitations that are associated with microarray-based analyses of Tissue samples collected during surgery as well as biopsies are often fixed in Formalin and embedded in Paraffin (FFPE)
Summary
Tissue samples collected during surgery as well as biopsies are often fixed in Formalin and embedded in Paraffin (FFPE).Molecular genomics assays on archived FFPE blocks, together with clinicopathological information, can provide critical insights into a heterogeneous disease like breast cancer, especially considering the fact that FFPE samples are the most widely available source of tissue material for which long-term clinical follow-up data are recorded. Tissue samples collected during surgery as well as biopsies are often fixed in Formalin and embedded in Paraffin (FFPE). Gene Expression Profiling of Paraffin Tissue the availability of both FFPE (Formalin Fixed Paraffin Embedded) and FF (Fresh Frozen) material. For these patients, we collected 21 individual FFPE blocks and 21 individual snap frozen diagnostic biopsies. Frozen (FF) RNA using this platform is lacking To this end we profiled, in duplicate, 20 FFPE tissues and 20 matched FF tissues and evaluated the concordance of the DASL results from FFPE and matched FF material
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