Abstract
Formalin fixed paraffin-embedded (FFPE) tumor specimens are the conventionally archived material in clinical practice, representing an invaluable tissue source for biomarkers development, validation and routine implementation. For many prospective clinical trials, this material has been collected allowing for a prospective-retrospective study design which represents a successful strategy to define clinical utility for candidate markers. Gene expression data can be obtained even from FFPE specimens with the broadly used Affymetrix HG-U133 Plus 2.0 microarray platform. Nevertheless, important major discrepancies remain in expression data obtained from FFPE compared to fresh-frozen samples, prompting the need for appropriate data processing which could help to obtain more consistent results in downstream analyses. In a publicly available dataset of matched frozen and FFPE expression data, the performances of different normalization methods and specifically designed Chip Description Files (CDFs) were compared. The use of an alternative CDFs together with fRMA normalization significantly improved frozen-FFPE sample correlations, frozen-FFPE probeset correlations and agreement of differential analysis between different tumor subtypes. The relevance of our optimized data processing was assessed and validated using two independent datasets. In this study we demonstrated that an appropriate data processing can significantly improve the reliability of gene expression data derived from FFPE tissues using the standard Affymetrix platform. Tools for the implementation of our data processing algorithm are made publicly available at http://www.biocut.unito.it/cdf-ffpe/.
Highlights
Gene expression profiling has proved to be successful in cancer research [1]
Formalin-fixed paraffin-embedded (FFPE) tissue specimens are collected for clinical routine diagnostics almost everywhere allowing a broader clinical implementation of biomarkers developed from such source of material
To verify the effect of RNA degradation on probe signals, we focused on the distance from the 39-end of the 11 probes in each standard Affymetrix probeset in the Williams dataset
Summary
The first pivotal studies [2,3] have been conducted using fresh-frozen samples as source of RNA since commercially available whole gene expression platforms were designed for high quality RNA. The need of fresh-frozen samples has represented one of the major limiting factors in biomarker discovery, development, validation and clinical implementation since few tissue banks with frozen specimens linked to clinical meaningful information were available [4]. Formalin-fixed paraffin-embedded (FFPE) tissue specimens are collected for clinical routine diagnostics almost everywhere allowing a broader clinical implementation of biomarkers developed from such source of material. The commercially available tool Oncotype DX which is broadly used in the clinical practice for breast cancer patients has been validated so far only using retrospectiveprospective studies design [6]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
