[Genome] genomic sequence marker

[Baojin Fu]

We've identified a amplified region on one human chromosome using
microarray technique. Next we'd like to confirm this amplified region
using quantitive real-time pcr. Therefore I need to design at least
three set of primer pairs: one locacted within , one up- and one
downstream of the amplified region. Then using a normal diploid cell as
control I should be able to quantify the copy number of the target
region. 
Now my question is: I have to use genomic sequence as template to
design PCR primer. The sequence must be human specific and unique (no
redundant, for example). What kind of sequence I should use? Can I
randomly choose a fragment of the sequence within my interested region
and then do a BLAST to make sure it's both human specific and unique? Is
this a valid way to do this? Or there is some known genomic "markers"
(not genes) on the chromosome, which is unique in sequence and suitable
for PCR primer design? If this is true, how can I search/locate them?

Thanks a lot.



Baojin Fu  M.D.
Research Assoicate
Division of GI/Liver Pathology
Johns Hopkins University School of Medicine
CRB-II, Ste 316
1550 Orleans St
Baltimore, MD 21231
Tel: 410-955-3511
Fax: 410-614-0671