Abstract
Abstract Formalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research and clinical setting. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. In this study, we profiled, in duplicate, 20 FFPE breast cancer tissues and 20 matched FF tissues and evaluated the concordance of the gene expression results from FFPE and matched FF material using the whole Genome (WG) DASL assay. We show that clinically relevant biomarkers developed on FF samples can be applied to FFPE samples. We show that after proper normalization, all FFPE and FF pairs exhibited 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 G/C content percentage and were enriched for cell cycle genes. Predictions of gene expression signatures developed on frozen material (Intrinsic subtype, Genomic Grade Index, 70 gene prognosis signature) show a high level of concordance between FFPE and FF matched pairs. Predictions based on a 60 gene DASL list (best match with the 70 gene signature) show very high concordance with MammaPrint® results. We demonstrate that data generated from FFPE material with the DASL assay, if properly processed, are comparable to data extracted from the FF counterpart. 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. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4834. doi:10.1158/1538-7445.AM2011-4834
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