FFPE Paraffin Removal and Extraction

Covaris AFA® technology provides a patented and unique methodology to efficiently emulsify and remove paraffin from an FFPE sample, freeing and exposing more tissue. This allows superior accessibility to the tissue during biomolecule extraction, enabling a higher quality purification.

Extract high-quality DNA, RNA, and Proteins from FFPE tissue samples

Formalin fixation and paraffin embedding (FFPE) is the most common method of preserving and archiving solid tissues. The extraction of biomolecules from FFPE tissue samples can often be challenging due to the quality of the stored sample. Covaris offers a range of FFPE extraction kits for your specific biomolecule extraction workflow needs, including both bead-based and column kits.
Covaris FFPE extraction, powered by Adaptive Focused Acoustics® (AFA®) technology enables:
  • Superior extraction for low mass inputs from slides and cores
  • Hands-free paraffin removal – no toxic organic solvents required
  • Extraction of longer RNA with high DV200 scores – detect rare fusion events
  • Reduced variability with a simplified and standardized workflow
  • Semi-automated, high-throughput processing


“Deparaffinization of FFPE tissue in the Covaris E220 allows us to avoid the use of xylene in our small laboratory space. Paraffin is efficiently removed from FFPE samples, removing any concerns of clogging columns, contaminating instrumentation or suppressing ionization.”
Dr. J. Chapman

Laboratory Director, Memorial Sloan-Kettering

Simultaneously Extract NGS-quality DNA and RNA from FFPE Tissue Samples

truXTRAC Total Nucleic Acid kits use AFA® technology to actively and concurrently extract both DNA and RNA from formalin-fixed, paraffin-embedded (FFPE) tissue in an aqueous buffer. This dual extraction workflow has been designed to maximize recovery of intact nucleic acids, allowing researchers to detect low frequency mutations and rare gene fusion events.


Learn more in our truXTRAC FFPE total nucleic acid flyer.

High-Quality RNA Results

FFPE RNA quality from precious clinical samples have the potential of impacting all downstream analytical applications. FFPE RNA extraction with Covaris is superior for scrolls, cores, and low mass inputs from slides. The improved extraction workflow leads to longer RNA yields with high DV200 scores allowing you to detect rare fusion events and lower your QNS rate.

Results are derived from an optimized protocol that is available solely as a service through Discovery Life Sciences' sequencing and bioinformatics laboratory - HudsonAlpha Discovery. (Levy, S. The ORIEN Project- Large Scale Integration of FFPE Material into a Multisite Research Alliance. Oral presentation at AACR 2019; April 1, 2019).


Learn more about the benefits of FFPE RNA extraction with Covaris in the FFPE RNA Quality Application Note.
An excerpt from the presentation: The ORIEN Project- Large Scale Integration of FFPE Material into a Multisite Research Alliance
Presented by Shawn Levy, PhD, Faculty Investigator, Discovery Life Sciences
Interested in learning more about Discovery Life Sciences’ workflow with Covaris truXTRAC FFPE technology? Watch the full video.

Empowering improved diagnostic decisions through an automated clinical FFPE extraction workflow

Formalin-fixed, paraffin-embedded (FFPE) methods are the preferred way to archive clinical tissue biopsy samples for histopathological diagnosis. As advances in clinical molecular pathology continue, there is an increasing need for reliable FFPE extraction methods from FFPE tissue specimens. However, nucleic acid extraction from FFPE samples can be challenging and labor intensive, often resulting in degraded and fragmented DNA.
OmniSeq® was founded to advance personalized medicine through their offering of New York State CLEP approved comprehensive molecular profiling, as well as offer a wide variety of pharmaceutical services to assist in drug development. OmniSeq utilizes Covaris AFA-energetics platform technology and truXTRAC® FFPE kits in their extraction workflows for higher extraction yields and quality DNA and RNA from FFPE samples, allowing physicians and clinicians to receive actionable results, and their patients to receive a more accurate diagnosis.
A Novel Solution to FFPE Extraction Challenges for Downstream Clinical Assays
Presented by: Sean Glenn, PhD, Vice President Clinical and Research Development, OmniSeq
The efficiency and reproducibility of their co-extraction workflow enabled OmniSeq to increase throughput to a point where automation was required. Covaris and Dynamic Devices collaborated to successfully design and build a custom automated extraction platform using the integration compatible Covaris LE220R-plus Focused-Ultrasonicator and Dynamic Devices Lynx LM1200 Liquid Handler. The result was a standardized clinical FFPE extraction workflow providing higher confidence in their downstream results with higher yields and corresponding higher DV200 scores, increased efficiency, decreased sample variability and reduction on manual “touchpoints” throughout the process. Click here to learn more about Covaris automated sample preparation capabilities.

“In collaboration with Covaris and Omniseq, we automated Omniseq's clinical FFPE DNA and RNA co-extraction workflow, improving their scalability and throughput. The combination of Covaris' AFA technology for extraction and Dynamic Devices Lynx's ST96 Pipettor with iPAW gripper arm produced complex movements and robust pipetting for dealing with difficult or variable sample types. This all enabled the workflow to be reproducible and accurate for the required diagnostic tests.”
Jeff Kent

Dynamic Devices

Protein Extraction from FFPE Tissue

A simple, efficient, and optimized proteomics workflow is also enabled by Covaris AFA technology. The protocol developed for protein extraction from FFPE material drastically improves sample preparation by actively removing more paraffin while rehydrating tissue to isolate proteins prior to purification.

Covaris AFA Paired with S-Trap Columns

FFPE Protein Extraction Workflow with S-Trap



  1. V Pestinger, et al. - 2020 Use of an integrated pan-cancer oncology enrichment NGS assay to measure tumour mutational burden and detect clinically actionable variants
  2. Robbe, et al.- 2018 Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project
  3. Calsina B, et al. - 2018 Role of MDH2 pathogenic variant in pheochromocytoma and paraganglioma patients.
  4. Edmund CP Chedgy, et al. - 2018 Biallelic Tumor Suppressor Loss and DNA Repair Defects in de novo Small Cell Prostate Cancer
  5. Stine H. Kresse, et al. - 2018 Evaluation of Commercial DNA and RNA Extraction Methods for High-Throughput Sequencing of FFPE Samples
  6. Carsten Holzmann, et al. - 2018 Malignant Transformation of Uterine Leiomyoma to Myxoid Leiomyosarcoma After Morcellation Associated with ALK Rearrangement and Loss of 14q
  7. Catherine Zilberg, et al. - 2018 Analysis of Clinically Relevant Somatic Mutations in High-Risk Head and Neck Cutaneous Squamous Cell Carcinoma
  8. Jeffrey M. Conroy, et al. - The Journal of Molecular Diagnostics, 2018 Analytical Validation of a Next-Generation Sequencing Assay to Monitor Immune Responses in Solid Tumors
  9. Katrin Bankov, et al. - Clinical and Translational Gastroenterology, 2018 Sequencing of Intraductal Biopsies is Feasible and Potentially Impacts Clinical Management of Patients with Indeterminate Biliary Stricture and Cholangiocarcinoma
  10. Brannan B. Griffin, et al. - International Journal of Surgical Pathology, 2017 Malignant Ectomesenchymoma: Series Analysis of a Histologically and Genetically Heterogeneous Tumor