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Too Good to be True- RNA Extraction from FFPE for NGS

"The first time the senior scientist in the lab showed me the data, I thought, well there's absolutely no way this is real so run it again on another set of samples, and run it again on another set of samples, and this exact pattern continues to repeat."- Shawn Levy

The ORIEN Project- Large Scale Integration of FFPE Material into a Multisite Research Alliance

Presented by
: Shawn Levy, PhD, Faculty Investigator for HudsonAlpha Institute for Biotechnology, at ABRF 2019 & AACR 2019.

Key Takeaways using the Covaris truXTRAC® FFPE Total Nucleic Acid Magnetic Bead Kit:
  • 85-90% of Covaris extracted samples have DV200 >30%, the cutoff for Illumina RNA Input for NGS 
  • 5-20% of samples extracted using traditional means have DV200>30%
  • DV200 is the percent of RNA extracted of length greater than 200 nt, a key Illumina NGS metric
  • Higher quality of extracted RNA translates to sequencing more samples with better RNA-Seq data for faster turnaround times
 
 

High Performance Multiplexed Whole Exome Sequencing from Problematic FFPE Tissues
Sequence previously unsequenceable FFPE samples

Presented by: Twist Bioscience and Covaris at AACR 2019 

Key Takeaways:
  • Covaris and Twist together allow for sequencing of challenging FFPE samples (Q305 / Q41 ratio <0.2), heretofore unsequenceable, with unmatched uniformity and 30X depth of coverage values
  • The Covaris truXTRAC FFPE tNA plus kit (magnetic bead-based) allows users to actively extract DNA in a simple, automatable workflow without the use of organic solvents
  • DNA can be sheared with Covaris Adaptive Focused Acoustics® (AFA®) to defined sizes, ready to use for library prep 
  • The Twist Mechanical Library Preparation Kits are compatible with Covaris AFA shearing and generate high-quality libraries ready for targeted capture or direct sequencing
 
 
 

Automate FFPE Extraction of Clinical Samples and Reduce QNS Rates
High Throughput Total Nucleic Acid Profiling of FFPE Tumors

Presented by: Sean Glenn, PhD, Vice President Clinical and Research Development, OmniSeq

Covaris Adaptive Focused Acoustic® technology when combined with the truXTRAC FFPE Total Nucleic Acid kit enabled OmniSeq to:
  • Improve QNS rates from >15% to <5%
  • Reduce result variability from inherently complex clinical samples
  • Integrate liquid handling automation to reduce sample workflow touch points
  • Extract DNA and RNA from a single precious sample to run many genetic tests
 
Featured FFPE Publications


Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project


Robbe et. al. found that using Covaris truXTRAC FFPE kits to extract DNA from cancer samples produced optimized and favorable results as an alternative source of DNA for WGS cancer diagnostics if flash frozen tissue was unavailable.
doi:10.1038/gim.2017.241
 

 
 

Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples


Kresse et. al. found that when using Covaris truXTRAC FFPE DNA Kit they were able to extract higher DNA yields and increase gene fusion detections. 
doi:10.1371/journal.pone.0197456
 

 
Application Notes & Resources

Nucleic Acid Extraction from Laser-Capture Microdissected (LCM) FFPE Tissues
 

    

A Streamlined Workflow to Perform ChIP from FFPE Samples
 

 
truXTRAC FFPE Kits Web Page

 
truXTRAC FFPE Kits Selection Tool

Are you unsure of which kit best fits your workflow? Try our FFPE Kit selection tool to discover the answer!

      

Contact Covaris Today!

applicationsupport@covaris.com

techsupport@covaris.com

customerservice@covaris.com

Upcoming Events

SFAF 2019| May 21-23

Santa Fe, New Mexico

Covaris Tech Talk & Poster:

May 21, 2019| 4:50pm


Sample to NGS Library:  Adaptive Focused Acoustics® (AFA®)-Enhanced Lysis and Lysate Homogenization for High-Throughput Nucleic Acid Extraction

Presenter:

Uli Thomann, Senior Director R&D, Covaris  

Contact Us:
Tel: +1 781-932-3959
Fax: +1 781-932-8705
info@covaris.com

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