2016 ADX
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SC1 Overcoming Challenges of Working with FFPE Samples   


9:00 Opening Remarks 

Mickey WilliamsModerator: P. Mickey Williams, Ph.D. (Contractor), Director of Molecular Characterization and Clinical Assay Development Laboratory (MoCha), Frederick National Laboratory for Cancer Research 



9:05 Biospecimen Pre-Analytical Factors and Best Practices 

Helen M. Moore, Program Director, Biorepositories and Biospecimen Research Branch, NCI NIH


9:45 Comparison of Methods for Preserving Morphological, Molecular, and Protein Biomarkers in Tissue 

Keith Moskowitz, Ph.D., Director, Diagnostics, Pre-Analytical Systems, BD Diagnostics

Formalin fixation of tissue is the standard for preserving tissue morphology, but proteins and nucleic acids are cross-linked, creating problems for the use of FFPE tissues with modern molecular technologies.  Cryopreservation preserves protein and nucleic acid biomarkers, but is less than optimal for studying tissue morphology.  In this workshop, FFPE and cryopreserved tissue will be compared to the PAXgene Tissue System, a non-formalin fixative for the preservation of morphology, DNA, RNA proteins and phosphoproteins in tissue.    


10:25 - 10:40 Coffee Break 


10:40 Assay Development of DNA Extraction Methods Using Fixed Tissues 

Helen Y. Wu, Ph.D., Project Leader, Genomics and Oncology, Roche Molecular Systems

The presenter will discuss the importance of a robust validated DNA extraction method for use with FDA approved mutation detection oncology tests developed by Roche Molecular Systems. In addition, performance of the cobas® DNA Sample Preparation Kit with challenging specimens will be discussed.



11:20 Working with FFPET Specimens: A Microarray Assay for Lymphoma Diagnosis, a New Hybridization Based Method for Digital Gene Expression Using FFPET and NGS from FFPET Specimens 

 Jason LihJason Lih, Ph.D. (Contractor), Principal Scientist, Molecular Characterization & Clinical Assay Development Laboratory, SAIC Frederick National Laboratory for Cancer Research, SAIC-Frederick

Overcoming poor quality in FFPE derived nucleic acids is one of the major challenges in molecular assays performed on cancer specimens.  I will present a method of assessing quality of FFPE nucleic acids prior to NGS assays and a study of molecular classification Non-Hodgkin’s Lymphoma by applying new technologies to profile gene expression using FFPE RNA samples. The talk will focus on experience of working FFPE in assay development and quality checks.


12:00 Close of Course   


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