Successfully Overcoming the Challenges of Working with FFPE Samples

  • Discuss the challenges that need to be addressed for success
  • Approaches to consider for optimizing your research


Formalin-fixed paraffin-embedded (FFPE) tissue samples are a valuable source of genetic information for gene expression and clinical research. Extraction of nucleic acid from FFPE tissues is a challenge because the fixation process results in cross-linking between proteins and nucleic acid, as well as between different strands of DNA or RNA molecules. Damage to the nucleic acid also results in a high degree of fragmentation making it difficult to extract nucleic acid that is suitable for downstream applications such as genotyping, gene expression profiling and Next Generation Sequencing.

Recent advances in sample preparation now enable access to the valuable information contained within these difficult samples. In our webinar we will discuss FFPE samples, the challenges that need to be addressed for success, and approaches to consider for optimizing your research, including:

  1. Fixation and embedding
  2. Nucleic acid extraction
  3. Weighing the pros and cons of different quantitation systems
  4. Analysis of FFPE samples by qPCR
  5. Suitability for other demanding downstream assays such as sequencing



Trista Schagat, PhD
Scientific Applications Manager

Dr. Trista Schagat is the Manager of Scientific Applications at Promega Corporation.  Dr. Schagat started her career at Promega in the Technical Services department before moving to the Scientific Applications group, which focuses on the development of new applications for existing products in response to customer requests.  Prior to joining Promega, she received her Ph.D. in 2000 from the Cell Biology Department at Duke University where she studied the role of pulmonary surfactant proteins in innate immunity.  She followed her thesis work with postdoctoral training in the Department of Medical Microbiology at the University of Wisconsin – Madison.  In addition to managing the global Scientific Applications team, Dr. Schagat is an adjunct Research Investigator at the University of Michigan Medical School in the Department of Biological Chemistry where she applies Promega technologies to study mechanisms that regulate RNA stability and expression.

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