ffpe

The "ffpe" (formalin-fixed, paraffin-embedded) software tool is designed to overcome the challenges of using formalin-fixed, paraffin-embedded (FFPE) tissue samples for transcriptional profiling. This task has historically been hindered by RNA degradation. With the advent of new, highly sensitive assays for whole-transcriptome microarray analysis of FFPE tissues, there's a need for advanced quality control (QC) methods to address the inherent noise and variability in the resulting data.

"ffpe" was developed in the context of the most extensive whole-genome expression studies from FFPE tissues to date, encompassing 1,003 colorectal cancer (CRC) and 168 breast cancer samples, along with a meta-analysis of 14 new and published FFPE microarray datasets. This tool introduces novel QC methods validated through various rigorous approaches, including technical replication, comparison with fresh-frozen tissue data, and the recovery of known gene expression-protein abundance associations.

The QC methods focus on assessing the sample dynamic range and the median profile per study, enabling stringent criteria for data analysis. Through these refined QC techniques, "ffpe" successfully identifies gene signatures relevant to microsatellite instability, among other features in CRC, and it enhances the association between gene expression and protein abundance for key biomarkers.