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FFPE Tissue and the HTG EdgeSeq Oncology Biomarker Panel

The overwhelming majority of archival samples of cancer tissue are formalin-fixed, paraffin-embedded (FFPE).  Many FFPE samples, especially pre-treatment biopsy specimens, are too small to reliably extract sufficient RNA for gene expression analysis.  HTG Molecular recommends 12.5 mm2 of tissue from one 5 μm FFPE section with no RNA extraction necessary for gene expression data from their HTG EdgeSeq nuclease-protection assay.

HTG EdgeSeq Oncology Biomarker Panel covers 2,560 genes.  This pilot study examined different amounts of tissue input from 3 colorectal and 2 breast tumors down to 3.1 mm2, representing ¼ the recommended input.

During this webcast you will learn/our speaker(s) will address:

  • The HTG EdgeSeq Oncology Biomarker Panel provides a solid platform to obtain gene expression data from FFPE samples far too small for reliable RNA extraction. 
  • Reproducibility was robust, with technical replicates correlating >0.98, and small areas of the tumor correlating very well with each other, and reasonably well with NanoString and TaqMan data from extracted RNA.
  • The lower limit for tissue input for this assay was not reached in this experiment, but most FFPE biopsy samples of interest will not be smaller than 3.125 mm2


Katherine Pogue-Geile, Ph.D., NSABP

Speaker Biography

Dr. Katherine (Kay) Pogue-Geile is Associate Director of MicroArray/Molecular Profiling at the National Surgical Breast and Bowel Project (NSABA) in Pittsburgh, PA.  She has 30 year’s experience in cancer research using a variety of molecular techniques to elucidate molecular mechanisms involved in cancer.  At the NASBP, Dr. Pogue-Geile has developed methodologies for profiling DNA and RNA utilizing formalin fixed paraffin embedded tissue (FFPE) samples collected in clinical trials to identify and validate biomarkers for prognosis and prediction of response to therapy in colon and breast cancer.

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