Genechip p53 sequencing
cgriffin at wco.com
Fri Mar 23 02:59:32 EST 2001
I have performed GeneChip analysis using the p53 arrays and fixed DNA
with success in the few analysis I've had occasion to perform, however I
found that in some cases the initial multiplex PCR rxn was insufficient,
and a second amplification was needed. I would imagine the extent of
fragmentation suffered by the final sample may be the determining factor
with respect to the need for re-amplification. Affymetrix in fact does
point out that DNA isolated from fixed tissue may in fact require a
second round of amplification, so even the company is aware of the issue
and has presumably performed some level of in-house R&D to address the
matter. Overall it is my experience that for all the p53 multiplex rxns.
it is very useful to run a sample of a known quality multiplex rxn as a
standard in electrophoresis to which one can compare the fixed samples.
With the reference intensity provided one can gain some sense of the
extent to which the PCR was a success.
I hope this helps, and good luck.
P.S. Do you per chance know a dear friend of mine -Dr. Alberto Sechi, he
is based in Udine?
Mol. Biol. GCRC Core
email: aniya at itsa.ucsf.edu
In article <3A9D1656.B07A4E0E at cmns.mnegri.it>,
Emanuela Guerra <guerra at cmns.mnegri.it> wrote:
> I would like to know if p53 sequencing using DNA chips works with
> formalin-fixed, paraffin embedded tumor samples - the DNA I get from
> these is very heavily fragmented, and I wonder if it amplifies well
> enough in the initial multiplex PCR...Anyone can help?
> Emanuela Guerra
> Consorzio Mario Negri Sud
> S. Maria Imbaro (Ch)
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