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September 19, 2019

Unlocking the Transcriptomic Potential of FFPE Cancer Samples: A Cross-Platform Comparison Study

Genome Webinar

Postdoctoral Research Fellow,
Cancer Research UK Edinburgh Center,
MRC Institute of Genetics and Molecular Medicine

This webinar discusses a study that compared nine different transcriptomic analysis technologies with matched fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) cancer tissues.

Cost and tissue availability normally preclude processing samples across multiple technologies, making it difficult to directly evaluate performance, reliability, and to what extent gene expression data from different platforms can be compared or integrated. In order to explore the feasibility of integrating gene expression data from different platforms, Dr. Arran K. Turnbull of the Cancer Research UK Edinburgh Center and colleagues explored nine technologies, which varied in resolution, cost, and RNA requirements.

The study used sequential tumor biopsies from 11 postmenopausal women with estrogen receptor positive breast cancer treated with three months of neoadjuvant anti-estrogen therapy. Half of each sample was snap frozen in liquid nitrogen and half was FFPE.

Transcriptomic analyses were performed using the Illumina Beadarray, Affymetrix U133A, Affymetrix Clariom S, NanoString nCounter, AmpliSeq Transcriptome, Lexogen QuantSeq and IonXpress RNAseq, Tempo-Seq BioSpyder, and Qiagen UPX 3’.

 Dr. Turnbull details the study’s findings, which include: 

  • Robust gene expression profiles can be reliably generated from FFPE tissues and are comparable to those derived from FF tissue using established transcriptomic approaches.
  • A range of new technologies are available for the study of FFPE tissues; these vary in cost, resolution, and RNA requirements to fit the user’s needs.
  • Gene expression data from biologically similar studies, generated using different technologies, can be reliably integrated for robust meta-analysis, subject to appropriate batch correction analysis.