DNA Microarrays with materials from paraffin blocks - (Nov/20/2005 )
Can I do DNA microarrays with materials in paraffin blocks? Someone have the protocol?
What do you want to study with DNA?
The only problem with DNA extracted from paraffin blocks is the possibility of DNA degradation. DNA strands may be broken into fragments of hundreds bps. If that is not a problem, why not?
I had DNA from FFPE tissue (extracted several years ago by standard fenol/chlorophorm method) and except from other methods I wanted to use DNA-chip as well. Unfortunately, I did not get any usefull data out of it. Our core facility that (I suppose) is specialized to work with Affymetrix microarrays claimed my tumor sample was too bad to proccess (I was comparing normal and tumor DNA from 1 patient). It's funny but I had pretty good results from this sample from microsatellite analysis...
Anyway, I gave up. I was not able to convince the techs my sample was OK. Even greater DNA fragmentation should not be a problem so I was clueless. But I encourage you to try it. Use one sample (the best one you have) a give it a try. What do you expect from DNA microarray?
I’m thinking try compare different types of thyroid tumor chosen genetics alterations and try to correlate whit prognostic.
All this materials are biopsies from patient’s that made thyreoidectomie
If you do WGA (whole genome amplification) first you should have lots of DNA to use in your DNA arrays. One in my lab have had pretty good succes using the Genomeplex kit on parafin blocks.