(SW4) Use of FFPE in Next-Generation Sequencing: Considerations from Bedside to Bench

Location: 213B

Archival formalin fixed, paraffin embedded (FFPE) samples are increasingly becoming attractive sources of nucleic acid material in the scientific community; these samples often have extensive metadata attached to them with respect to clinical treatments and outcomes, and they often times provide the most feasible method to study rare, difficult to access, or quickly progressing tumor types where accumulating live study participants is onerous or impossible on a reasonable time scale.  However, these samples are notoriously difficult to extract, evaluate for quality control and use in preparing next-generation sequencing (NGS) libraries. In this seminar, participants will become familiar with all aspects of the FFPE process, including methods of preservation; pre and post fixation variables that can affect nucleic acid quality; and best practices for nucleic acid extraction and quality assessment, NGS library preparation, sequencing, and bioinformatic analysis. Target audience is scientists, predominantly in genomics and bioinformatics, but also potential interest from proteomics, flow cytometry, and pathology disciplines.

Marie Adams, Van Andel Institute
Zach Herbert, Dana Farber Cancer Institute

Bill LaFramboise, PhD; Chief Genomics Technology Officer, Allegheny Cancer Institute
Hamid Khoja, PhD; Covaris
Han Wei, PhD; Beckman Coulter
Prashant Singh, PhD; Roswell Park Comprehensive Cancer Center
Katie Hoadley, PhD; University of North Carolina
Scott Tighe, PhD; Vermont Intregrative Genomics Facility
Shawn Levy, PhD; HudsonAlpha Institute for Biotechnology

Click here for registration information.

Workshop Schedule:

8:00 AM - 8:15 AM Introduction and Welcome  (Marie Adams, DSRG Chair )
8:15 AM - 9:15 AM Pre and Post Analytical Variables – the Pathology of FFPE Samples (Bill LaFramboise, PhD; Chief Genomics Technology Officer, Allegheny Cancer Institute)
9:15 AM - 10:00 AM FFPE Isolation Techniques Part 1:  Isolation by Acoustic Shearing (Hamid Khoja, PhD; Covaris)
10:00 AM - 10:30 AM Coffee Break
10:30 AM - 11:15 AM FFPE Isolation Techniques Part 2: Isolation by Magnetic Beads(Han Wei, PhD; Beckman Coulter)
11:15 AM - 12:00 PM

FFPE Considerations in NGS Library Preparation (Prashant Singh, PhD; Roswell Park Comprehensive Cancer Center) 

12:00 PM - 1:00 PM  Lunch 
1:00 PM - 2:00 PM FFPE Sequencing and Bioinformatics (DNA and RNA) (Katie Hoadley, PhD; University of North Carolina)
2:00 PM - 2:30 PM Coffee Break
2:30 PM - 3:15 PM Case Study: The Orien Project – Large Scale Integration of FFPE Material into a Multisite Research Alliance (Shawn Levy, HudsonAlpha)
3:15 PM - 3:55 PM Panel and Open Discussion – FFPE Materials in Cores; How Do We Make a Judgement Call on Sample Quality?
Bill LaFramboise, PhD
Hamid Khoja, PhD
Prashant Singh, PhD 
Katie Hoadley, PhD
Shawn Levy, PhD
Scott Tighe, PhD, Vermont Integrative Genomics Facility
3:55 PM – 4:00 PM Seminar Wrap Up 

Giga Level Sponsors

beckman coulter

Deca Level Sponsor