Next Generation Dx Summit

Short Course 1
Overcoming Challenges of Working with FFPE Samples
Monday, August 18 | 9:00am - 12:00pm

This course will provide important insights for overcoming challenges of working with FFPE samples for cancer research, including measuring the quality of DNA and its impact on NGS data, detecting RNA and profiling miRNA expression. Next generation sequencing (NGS) utilizes FFPE samples for clinical retrospective studies. Successful interpretation of the samples depends on the quality of the starting material. Participants will also learn how to understand the pre-analytic effects on RNA gene expression.

Instructors:

W. Fraser Symmans, M.D., Professor & Director, Research Operations, Pathology, UT MD Anderson Cancer Center

Sidney W. Fu, M.D., Ph.D., Professor & Associate Director, Genomic Medicine and of Medicine, Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences

Professor Beatrice S. Knudsen, M.D., Ph.D., Director, Translational Pathology, Cedars Sinai Medical Center

Topics to be covered

  • Understanding pre-analytic effects on RNA gene expression
  • Profiling miRNA expression
  • RNA detection in cancer tissues stored in FFPE samples
  • FFPE DNA quality control and its correlation with NGS data

Detailed agenda

9:00 am Understanding Pre-Analytic Effects on RNA Gene Expression from Fresh Samples and Applying it to FFPE

W. Fraser Symmans, M.D., Professor & Director, Research Operations, Pathology, UT MD Anderson Cancer Center

9:50 miRNA Expression Profiling Using FFPE Tissue

Sidney W. Fu, M.D., Ph.D., Professor & Associate Director, Genomic Medicine and of Medicine, Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences

Despite their rich clinical information including follow-up data, FFPE samples are not fully appreciated in mRNA expression analysis due to RNA degradation. miRNAs are a class of small non-coding regulatory RNAs that are involved in regulating target gene expression. miRNA expression profiling using FFPE tissue has proven to be a reliable technology.

10:10 Session Break

10:25 miRNA Expression Profiling Using FFPE Tissue (Continued)

Sidney W. Fu, M.D., Ph.D., Professor & Associate Director, Genomic Medicine and of Medicine, Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences

Despite their rich clinical information including follow-up data, FFPE samples are not fully appreciated in mRNA expression analysis due to RNA degradation. miRNAs are a class of small non-coding regulatory RNAs that are involved in regulating target gene expression. miRNA expression profiling using FFPE tissue has proven to be a reliable technology.

10:55 RNA Detection in Cancer Tissues Stored in FFPE Samples

Professor Beatrice S. Knudsen, M.D., Ph.D., Director, Translational Pathology, Cedars Sinai Medical Center

11:45 Q&A

12:00pm End of Short Course

Speaker Biographies

Fraser SymmansW. Fraser Symmans, M.D., Professor & Director, Research Operations, Pathology, UT MD Anderson Cancer Center

Dr. Fraser Symmans is Professor and Director of Research Operations in the Department of Pathology at University of Texas MD Anderson Cancer Center. His clinical diagnostic practice is in Breast Surgical Pathology and Cytopathology. Dr. Symmans received his medical degree from the University of Auckland, New Zealand in 1987. He completed his residency training in Anatomical Pathology at Columbia University College of Physicians and Surgeons, New York City and fellowship training in Cytopathology at MD Anderson Cancer Center. Dr. Symmans joined the faculty of New York University Medical Center in 1993 and moved to MD Anderson Cancer Center in 2000. Dr. Symmans's research is focused on breast cancer, with specific emphasis on neoadjuvant (pre-operative) treatment trials for evaluation of chemosensitivity and development of diagnostic tests to select the most effective treatments for individuals with breast cancer. Dr Symmans has adapted genomic technologies to clinical needle biopsies of breast cancer in order to use gene expression profiling to identify important genes for response to chemotherapy and, independently, to endocrine therapy; to validate gene expression tests with clinical potential; and to establish their performance in the context of clinical testing. In this capacity he directs a CLIA-compliant Pharmacogenomics Laboratory to support clinical trials. Dr. Symmans is also an active member within multicenter research collaborations, is a researcher for The Breast Cancer Research Foundation, currently a Komen Scholar, participates within the National Cancer Institute’s North American Breast Group (NABG) and the Breast International Group (BIG) where he co-chairs the Residual Disease Working Group and is a member of the Biomarkers Working Group and the Breast Oncology Local Regional (BOLD) Task Force, and is a member of the Tumor Biomarkers Panel For Advanced Breast Cancer of the American Society of Clinical Oncology (ASCO).

Sidney W. FuSidney W. Fu, M.D., Ph.D., Professor & Associate Director, Genomic Medicine and of Medicine, Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences

Dr. Sidney W. Fu is a professor, and associate director of Genomic Medicine in the Department of Medicine at the George Washington University. Dr. Fu’s main research is focused on cancer genomics, particularly in identifying and validating biomarkers for early diagnosis and treatment of breast cancer. Dr. Fu’s research program is currently funded by the NCI, Katzen Cancer Research award, Elaine H. Snyder Cancer Research Award and other private foundations.

Beatrice KnudsenBeatrice Knudsen, M.D., Ph.D., Medical Director, Translational Pathology, Cedars Sinai Medical Center

Beatrice Knudsen, M.D., Ph.D. is the Medical Director for Cedars-Sinai Advanced Biobank and Director of Translational Pathology at Cedars-Sinai Medical Center. She obtained her M.S. degree in Chemistry at University of Vienna, Austria and received her Ph.D. in Cell Biology and M.D. degrees at Cornell University, New York. She performed her post-doctoral fellowship in the Laboratory of Molecular Oncology at the Rockefeller University in New York and completed her residency in Anatomic Pathology at New York Hospital. Dr. Knusden is board certified in Anatomic Pathology. She has considerable experience with tissue procurement, tissue banking and molecular diagnostics. Further, she performs research in methods to improve quality of harvested tissues (for example, to stabilize phosphorylation and optimize other bioanalytes). In addition, she directs research programs on prostate cancer metastasis and prostate cancer prevention.

 

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