FFPE and FNA Tissue DNA/RNA Extraction


One challenge for molecular testing is extraction of DNA or RNA from FFPE tissue especially from a limited tissues such as FFPE FNA (fine needle aspiration).  The extraction methods on current market uses beads or column to bind/elute DNA or RNA. These methods cause significant loss of DNA / RNA during the extraction. TrimGen’s  WaxFreeTM method uses non-binding /elution approach to minimized the loss of DNA / RNA and give users an opportunity to maximize the downstream tests.  

TrimGen's WaxFree method uses a different approach 

Traditional beads or column extraction methods involved in bind-wash-elute steps.  When applied to FFPE tissuesbind-wash-elute steps cause a significant loss of DNA or RNA. TrimGen's WaxFree method eliminates the bind-wash-elute steps by using a special resin to remove PCR inhibitors and retains the DNA / RNA in extraction solution. The solution can then be directly used for PCR amplification.   

TrimGen's WaxFree method maximizes DNA recovery 

Four samples were used for following comparison. One consecutive FFPE section (about 1 to 1.5 cm2, 10 um thickness) is used for DNA extraction. 

Traditional beads or column based extraction methods lose DNA / RNA

  • DNA loss 1    The DNA in the FFPE tissues are short (average 200bp) and less charges.  these short DNA has low binding efficiency to the beads or column. 
  • DNA loss 2     Most of the DNA are washed off from beads or column due to weak binding capability. 
  • DNA loss 3     Some of DNA are permanently bind to the bead or column and cant elute from beads or column.

WaxFree method eliminated the DNA loss and maximized the DNA / RNA recovery from the FFPE samples

Next Generation Sequencing

With high DNA yields, the DNA extracted using TrimGen's WaxFree method provides excellent results for Next Generation Sequencing. The length and reads are higher than other methods.  WaxFree makes it easy to analyze the FNA sample using the NGS method. 

Non-toxic reagents are used

  • Most extraction kit use Xylene as a de-paraffin reagent. The Xylene is toxic and can cause systemic toxicity through inhalation. 
  • WaxFree kit uses a non-toxic reagent (Q-solution) for de-paraffin. The solution is safe for operator and the environment.

Widely used products

WaxFree products have been used for over 10 years in clinical test and in a broad range of research projects worldwide.  

See publication list

Related Products

Master Mix (GR060) - Special formulation with PCR  enhancer, this master mix shows excellent performance for FFPE DNA amplification.  High fidelity and robust.  

Mutation Analysis Reagents for Oncology – single platform for any somatic mutations.

Mutation Analysis Reagents - Next Generation Sequencing (NGS) platform 
 Traditional methodsWaxFree method
Final elute volume: 
DNA yield: 
Amount for PCR :  
Maxima assays: 
50 ul
0.2-0.6 ug
1-2 ul    
20-30 PCR assays
120 ul
1.5 - 3.2 ug
0.5-1 ul
200-300 PCR assays
"WaxFree method will give users an opportunity and capability to maximize downstream tests while using limited tissue resources."

                  Lane 1: Blank.     Lane 2: Genome DNA control
                  Lane 3-6: DNA extracted by WaxFree method
                  Lane 7-10: DNA extracted by Vendor Q method


The extracted DNA was used to amplify KRAS gene by PCR (35 cycles).

Upper panel- Input DNA for PCR: WaxFree method 1ul, Q-method 2 ul.

Lower panel- Input DNA for PCR: WaxFree method 0.5ul, Q-method 1 ul.

FNA (Fine Needle Aspiration) sample

One slide of FNA sample was used for DNA extraction. The DNA was collected in 60 ul optimized buffer.  3 ul of the DNA extracts was used for amplification of KRAS gene. From left 250 bp, 275 bp, 380bp, 495bp amplicons. The 60 ul of DNA extracted from one FNA slide is able to perform at least 20 times PCR assays.

"WaxFree method provides a fail-safe DNA extraction and the capability of high efficient PCR amplification ensuring success of your clinical test."  

Order Information

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Product Description





WaxFree DNA

WaxFree RNA

Quick Reference 

WF-20WaxFreeTM DNA 20 Extraction Kit20 preps 


WaxFreeTM DNA 50 Extraction Kit

50 preps

WF-100WaxFreeTM DNA 100 Extraction Kit100 preps
WR-20WaxFreeTM RNA 20 Extraction Kit20 preps
WR-50WaxFreeTM RNA 50 Extraction Kit50 preps

For research use only. Not for use in diagnostic procedures.