hello Mohammad Reza here is a manual protocol for extraction of DNA from formalin-fixed paraffin-embedded (FFPE) samples:

Materials:

• FFPE tissue block
• Reagents:
• 10 mM Tris-HCl, pH 8.0
• 0.5 M EDTA, pH 8.0
• 1% SDS
• Proteinase K
• 100% ethanol
• 70% ethanol
• TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0)

Procedure:

• Cut 4-5 10-micron sections of the FFPE tissue block and place them in a microcentrifuge tube.
• Add 500 μL of 10 mM Tris-HCl, pH 8.0, and 0.5 M EDTA, pH 8.0 to the tube.
• Incubate the tube at 60°C for 2 hours to melt the paraffin.
• Add 500 μL of 1% SDS to the tube and mix well.
• Add 100 μL of proteinase K (20 mg/mL) to the tube and mix well.
• Incubate the tube at 56°C overnight, or until complete lysis is achieved (up to 24 hours).
• Add 500 μL of 100% ethanol to the tube and mix well.
• Centrifuge the tube at 14,000 x g for 10 minutes.
• Pour off the supernatant and add 500 μL of 70% ethanol to the tube.
• Centrifuge the tube at 14,000 x g for 10 minutes.
• Pour off the supernatant and air-dry the pellet for 10 minutes.
• Resuspend the pellet in 100 μL of TE buffer.
• Store the DNA at -20°C for future use.

Note: The above protocol is a basic manual extraction method, but the DNA yield and quality may vary depending on the sample type and condition. If higher yields and better quality DNA are required, it is recommended to use a commercial kit specifically designed for FFPE DNA extraction.

Hello Mohammad Reza Eslami

I can totally understand your situation. A couple of years ago, we standardized a protocol for the extraction of DNA from archived H&E-stained slides. The same protocol can be modified and used for your application. Kindly find the paper for your perusal.

Hope this helps!

Article DNA extraction from archived hematoxylin and eosin-stained t...

Hi Mohammad Reza Eslami

Kindly use the following kit for DNA/RNA extractions from the FFPE, if affordability is not a big issue.

https://www.thermofisher.com/order/catalog/product/A31881

It is one of the best kits available, I never had any problem with this kit for FFPE case, if you follow well its entire protocol.

You do not need any special equipment for this like MagMax as it has manual protocol as well. Only thing you need are the magnetic racks.

https://www.thermofisher.com/order/catalog/product/12321D

Also if your lab does have a vacuum concentrator, which can fit 1.2 ml eppendorf centrifuge tubes then it rocks, alternatively you can use also room temperature-based drying protocol mentioned in this kit. You have quite good flexibility in this kit.

Regards....

Mansoor Khan

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Pushkal Sinduvadi Ramesh

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Jawwad Ahmad

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