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How to Automate DNA and RNA Extraction from FFPE Tissue

Nucleic acid extraction from FFPE (Formalin-Fixed Paraffin-Embedded) tissue can be a challenging process, whether conducted manually or using an automated workstation. The preparation of FFPE tissue results in low quantities of crosslinked and degraded nucleic acids, which have limited amplifiability. In this guide, you will discover how to automate the extraction of nucleic acids from FFPE tissue.

View this on-demand webinar for more information on how to efficiently build and troubleshoot an automated nucleic acid extraction workflow.

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Extraction from FFPE tissue can be broken into two major parts: preprocessing and purification. Preprocessing includes removing the paraffin, protein digestion, lysis and decrosslinking of nucleic acids. Subsequently, the nucleic acids are purified from the sample. You can automate the preprocessing of FFPE tissue samples or do it manually—there are advantages to both.

To learn about purification, refer to the detailed guide available in the "How to Automate Nucleic Acid Extraction" resource. In this comprehensive resource, you will find a video tutorial, guidance on experimental design for method development, and a troubleshooting guide that addresses each step.

Preprocessing Challenges

Preprocessing begins with loading samples into the well. However, due to the solid nature of FFPE samples, loading them into 96-well plates with blocks or curls can be challenging, tedious, and prone to cross-contamination. As a result, many laboratories choose to load these samples directly into individual tubes to minimize this risk. Your approach to preprocessing becomes crucial in light of this challenge. Some labs prefer manual preprocessing, while others opt for automated instruments. 

The next step involves adding a deparaffinization solution, such as xylenes, mineral oil, or other organic solvents, and applying heat to dissolve the wax. Transferring these organic solvents presents unique challenges in terms of liquid handling, as they do not behave like the aqueous solutions commonly encountered in biological research. If you choose to automate this step, we will explain how to optimize the liquid handling process for safe transfers in the "Aspirating and Dispensing Organic Liquids" section.

Following this step, you would typically add an aqueous digestion solution and proteinase K to facilitate sample digestion. These digestion processes typically take several hours, and you may opt for overnight incubation. Depending on the protocol, kit, and temperature parameters employed, there may also be a decrosslinking step. This step involves elevating the temperature to reverse the formalin-induced crosslinks.

Improving Preprocessing Efficiency

Preprocessing steps can be time-consuming and often tie up the instrument for extended incubations. Depending on your daily throughput requirements, you may need to consider alternatives. One approach is to maximize parallelization by performing preprocessing overnight and purification steps the following day. While this method is effective, it may require a larger platform and may not be the most efficient use of the instrument. Typically, labs either use a smaller instrument for preprocessing and transferring to a 96-well plate, or perform the initial steps manually. Your decision will be influenced by factors such as throughput needs, budget constraints, and available instrument space.

Manual Control Method

Before embarking on automating these steps, ensure you have a reliable manual magnetic bead-based protocol or kit that meets your specific requirements. This manual method will serve as a control for method development.

You will use this manual method as a benchmark to guide the development of each automated step. All observations and measurements will be relative to your manual control. Your goal is to reach the same performance as the manual control by teaching the robot how to manipulate the liquids and magnetic particles effectively.

If you need some tips to improve the performance of your manual methods, view this webinar for more information: "Successfully Overcoming the Challenges of Working with FFPE Samples

Aspirating and Dispensing Organic Liquids

The next step is to develop the liquid class for organic liquids in use. For more details on liquid class development, read "How to Build Liquid Classes". Since accuracy is not critical for dispensing organic liquids in this method, you can visually confirm that the action is occurring correctly without dripping, and estimate pipetting accuracy using another pipette.

If the kit uses mineral oil or a similar viscous organic liquid, follow these instructions:

  • Use a slow aspiration and dispensing rate.
  • Draw a small volume of air into the pipette before drawing up liquids to ensure complete liquid volume dispensing.
  • Pre-wet the pipettes by pipetting the liquid up 2 to 3 times before drawing up the desired volume. This will improve accuracy.
  • Draw extra reagent into the pipette to make sure the correct volume is dispensed.

If the kit uses xylene or a similar organic liquid, follow these instructions:

  • Draw a small volume of air into the handler’s pipette before drawing up liquids to help dispense the entire liquid volume.
  • After loading the pipette with liquid, draw up some air to prevent dripping. These liquids tend to have less cohesive force and may require more air to prevent dripping.

Lysis and Digestion

There are two different methods by which the next step can be completed. One approach is to first aspirate the dissolved paraffin, then perform lysis and digestion. Another approach is to perform the lysis and digestion without removal of the dissolved paraffin. Regardless of the approach you take, some oil may remain after dissolving the paraffin. Therefore, when you add the aqueous solution to perform lysis and digestion, be sure to gently mix the solution to prevent an emulsion from forming. This will help avoid the need for centrifugation to facilitate separation.

Tip: When adding the digestion solution and proteinase K, follow the manufacturer's instructions precisely. Be sure to add proteinase K directly to the sample to prevent it from losing activity by digesting itself, unless the manufacturer's protocol specifies otherwise.


When evaluating your nucleic acid extractions, consider the following:

  • UV/Vis absorbance tends to be inaccurate for highly degraded, low DNA-yielding samples, such as those from FFPE tissue (when DNA yields drop below 10 ng/µl, accuracy can decrease due to impurities).
  • Fluorescent dyes provide better quantitation than UV/Vis but may overestimate the quantity of functional, amplifiable nucleic acids.
  • Functional qPCR assays are preferred and are the most accurate measure of usable nucleic acid. Fluorescence measurements often overestimate usable nucleic acid by 2–3 times in degraded FFPE samples. This leads to incorrect normalizations and input for downstream applications such as NGS.

Downstream Predictive Value for Degraded Samples

Due to the inherent variability of FFPE DNA quality, knowing the quantity of DNA alone is not reliably predictive of downstream assay success. The ProNex® DNA QC Assay allows you to determine the amount of amplifiable DNA in a sample. You can use the ProNex® DNA QC Assay to evaluate if a sample is suitable for downstream analysis using techniques such as next-generation sequencing (NGS) or droplet digital PCR (ddPCR).



To learn about purification, refer to the "How to Automate Nucleic Acid Extraction" resource. In this comprehensive resource, you will find a video tutorial, guidance on experimental design for method development, and a troubleshooting guide that addresses each step.

A final recommendation on the extraction of DNA and RNA from FFPE tissue is to use a ring stand magnet and a low elution volume. This is particularly important because the resulting nucleic acid concentrations are typically lower compared to samples from normal tissue.

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