ffpe

ffpe provides quality control and analysis methods for gene expression data derived from formalin-fixed, paraffin-embedded (FFPE) tissue samples to enable reliable transcriptional profiling.

Key Features:

• Quality Control Metrics: Novel QC metrics tailored to FFPE-derived expression data quantify noise and variability arising from RNA degradation in archival samples.
• Concordance At the Top Plots (CAT-plots): CAT-plots visualize concordance at the top of gene expression rankings to identify low-quality or discordant samples.
• Dynamic Range and Median Profile Analysis: Sample dynamic range calculations and per-study median profile analysis assess transcriptional signal quality across studies of archival tissues.

Scientific Applications:

• Cancer Research: Applied to large-scale FFPE expression studies including 1,003 colorectal cancer (CRC) and 168 breast cancer cases to identify gene signatures such as those associated with microsatellite instability.
• Biomarker Discovery: Enhances recovery of associations between gene expression and protein abundance for biomarkers MLH1, FASN, CDX2, MGMT, and SIRT1 in CRC tumors.

Methodology:

Generation of CAT-plots, calculation of sample dynamic range, per-study median profile analysis, technical replication analysis, independent sample analysis, and comparison with fresh-frozen tissue results.