Short Courses and Special Courses

Clinical Application of Next Generation Sequencing for the Management of Patients with Solid Tumors

Monday, March 19, 2018 - 8:00 AM - 12:00 PM

Session Credits:

This session is not eligible for CME or SAM credit.

Course Director:

Jeffrey S. Ross, MD, Foundation Medicine, Inc., Cambridge, MA

Course Co-Director:

Neal I. Lindeman, MD, Brigham and Women’s Hospital and Dana Farber Cancer Institute, Boston, MA
Stephen Yip, MD, PhD, University of British Columbia and Vancouver General Hospital, Vancouver, BC

Course Description:

This half-day course is designed to familiarize the registrant with both the technical aspects and clinical applications of NGS for the solid tumor cancer patient. The first section of the course is organized into a didactic series of short lectures given by the course instructors to highlight the history of clinical DNA sequencing on cancer specimens focused on the search for potential therapy targets for patients with relapsed and refractory disease. The technical section will emphasize practical issues for pathologists including the types of samples that can be used, the quantity and proportion of tumor cells needed and the pre-analytic factors that can influence NGS test results. Both formalin fixed paraffin embedded tissues and blood-based “liquid biopsies” will be considered. The remaining sections of the course will consist of a case by case analysis that includes lung cancer, breast cancer, colorectal cancer, melanoma, brain tumors and cancer of unknown primary origin.

Learning Objectives:

Upon completion of this educational activity, learners will be able to:

  • Contrast the differences, advantages and disadvantages between next generation sequencing (NGS) technologies and traditional “Sanger Sequencing” methods
  • Understand the current limitations of “one off" single gene hotspot sequencing tests versus comprehensive genomic profiling by NGS
  • Contrast the advantages and disadvantages of the targeted NGS panel approach versus whole exome and whole genome sequencing
  • Understand how next generation sequencing technologies can be applied to detect all classes of genomic alterations including base substitutions, short insertions/deletions, fusions and translocations, and copy number alterations including amplifications and homozygous deletions in a clinical grade, regulatory agency approved (CLIA/CAP) format using routine clinical FFPE samples
  • Know how to preserve and prepare surgical pathology and cytologic samples including fluids and fine needle aspirations for NGS testing
  • Contrast the uses and limitations of using a blood sample for analysis of circulating tumor cell and cell free DNA for NGS
  • Be familiar with the potential of NGS to alter a cancer patient’s clinical outcome by identifying a genomic alteration that can lead to a specific targeted therapy that would not have been considered if the NGS results had not been available
  • Have a basic understanding of assessing quality assurance, proficiency testing and general validation of NGS procedures used in clinical testing of patient samples


8:00 AM Introductory Lectures: History of DNA Sequencing, Traditional and NGS Sequencing Technologies and the Roles of Pathologists in the Providing of NGS Results Designed to Direct Personalized Cancer Treatment
9:20 AM Case 1: Non-small Cell Lung Cancer
9:40 AM Case 2: Breast Cancer
10:00 AM Break
10:20 AM Case 3: Melanoma
10:40 AM Case 4: Colorectal Cancer
11:00 AM Case 5: Cancer of Unknown Primary Origin
11:20 AM Case 6: Brain Tumors
11:40 AM Questions and Discussion

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