I have FFPE samples from breast cancer tissue and I want to extract DNA for SNP genotyping by Real Time-PCR. What methods do you suggest for the extraction of DNA from FFPE samples?
YOu could try one of the QIAGEN kits for DNA extraction. These normally work quite well and are used routinely in our laboratory.
You can follow the protocol in the article bellow (Molecular diagnosis of nasopharyngeal carcinoma using detection of Epstein-Barr virus latent membrane protein-1 gene in cervical metastatic lymph nodes ). It is very fine.
Roche Kit, best, did tons of samples published the paper check in the paper.
I recommend Qiagen FFPE kits, I have tested it with RealTime PCR, it works very well
for more info call me or come to my office dear friend
Very thanks for all of friends. Qiagen and ambion FFPE kits have high cost and i want to try simple methods. we used RNXPlus kit for RNA extraction from 6years old FFPE sample and the results was interesting. Iwant to test phenol-chloroform for DNA. DNA extraction is easier than RNA extraction. likely DNA-protein phase can be mixed with chloroform.
I agree that Qiagen works great. We also use their deparafinization solution (it is blue and makes it easier to get remove supernatant). I have compared both the QIAamp DNA/RNA FFPE kit and the AllPrep kit. We get better results with the AllPrep. Slight differences in proteinase K concentrations and incubation times. We have used the DNA for droplet digital PCR and they look good.
I used Qiagen in the past, but found that depenindg on your technical staff an semi-automated system such as the Maxwell 16 works beter, less expensive as well. A quality extraction has a lot to do with the age of the speciment and how it was fixated as well. In general you shouldn't have problem and remember to keep your PCR fragments short. All the best.
if you want simple and low cost method, plese check my paper in my profile as:
3.
Characterization of human herpes virus 8 genotypes in Kaposi's sarcoma patients in Tehran, Iran.
I used Qiagen kit for FFPE samples and I used RNA free in the procedure so I can get btter DNA.
Dose anyone extract DNA from about 100 cells in FFPE samples captured by laser capture microdissection for DNA sequencing analysis? Which is better? Thanks a lot
I am working on prostate cancer ffpe tissues with deparaffinization solution and rna extraction kit of qiagen, but sample ODs are very low:( i really do not know what should i do with them:( I need your hepls my friends
Thanks for your considerations
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