Thursday, September 13, 2007

Tilescope not working

Is Tilescope working?

Currently Tilescope is going through some revisions and will be offline until further notice. Thank you for your patience.

Thursday, September 6, 2007

CK19 pseudogenes effect on primer design

I read with great interest your article "Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome" Genome Res. 2003 13:2541-2558. As I'm especially interested in CK19 pseudogenes, because we use this gene in the tumour biology department as a marker to detect tumour cells in lymph nodes of breast
cancer patients, I have a few questions to you and would be very grateful if you could answer them:

We designed our primers for the PCR approach in that way that the two pseudogenes (Genbank accession number M33101 (CK19a) and U85961 (CK19b)) mentioned in the literature cannot be amplified. You wrote in your article that there exist 4 pseudogenes of CK19 on chromosome 4, 6, 10 and 12. As we want to avoid false positive results in our detection approach it is very important for us to know the sequence of the other 2 pseudogenes. Could you provide us with the sequence or some further information on these pseudogenes – possibly the alignment of the CK19 sequence with the 4 pseudogenes? Do you know if CK19 pseudogenes can be transcribed? I looked in the literature and databases for this information but could not find an answer.

There are indeed 4 processed pseudogenes identified by the pipeline methodology developed in Dr. Gerstein's lab. You can retrieve the nucleotide sequences and the alignment of each pseudogene to CK19 from the following URL

I have also included one other potentially pseudogenic fragment upstream of CK19 at Chr 17. This is labeled 'ambiguous' as only a small portion matches to the parent gene. I have provided nucleotide alignments as I assume that is what is relevant for PCR purposes. Also, please note that all the pseudogenes are processed pseudogenes.