DNA IDENTIFICATION - HOW TO TELL THE DIFFERENCE (Feb/23/2009 )

could you probe for tumor markers?

perneseblue on Feb 25 2009, 03:05 PM said:

PCR of one gene, and then RFLP (restriction fragment lenght polymorphism). We are searching for LOH (loss of heterozygosity). I*m afraid if we get something, we wouldn*t be able to tell if it is really LOH or something else...(it could also be mutation or something else). There is no use of doing anything untill we find out what is what...
A second DNA? No, comparison is always done with a tumor and blood DNA of the same patient.

mdfenko on Feb 25 2009, 04:21 PM said:

Can you please give some example of how it is done?

It's a long shot, but the blood sample should contain genomic DNA that's undergone some somatic rearrangement at the Ig locus (antibody and TCR rearrangements). Simple in theory, but finding out where is a bit more problematic as it can happen at many different places and in different combinations including heavy chains and light chains. However, getting certain PCR combinations can give you an idea if you see shifting bands. Here's a reference...they were looking at lymphomas, but the principle should still be the same. Am J Pathol. 1995 September; 147(3): 806–814.

PMCID: PMC1870987
Copyright notice
Detection of clonal lambda light chain gene rearrangements in frozen and paraffin-embedded tissues by polymerase chain reaction.
R. Küppers, K. Willenbrock, K. Rajewsky, and M. L. Hansmann
Institute for Genetics, University of Cologne, Germany.

The other "long shot" has been mentioned before and it would be helpful to know what kind of brain tumor the DNA came from...glioma or other kind and doing some kind of quantitative assay to look for genomic amplifications or deletions (such as LOH, microsatellite instabilities, etc)

Ok, thanks!

This is great...I feel like Sherlock Holmes...We*ll try to solve a problem and use some of the suggested options.