Dinucleotide Repeat PCR

[LICHY at EMAIL.AFIP.OSD.MIL]

        We have been analyzing tumor DNA samples for loss of heterozygosity by 
PCR of dinucleotide repeat polymorphisms.  In addition to products of the 
correct size, these reactions generate a substantial background ladder of 
products, mostly ranging in size from 5 bases shorter to 5 bases longer than the
size of the major reaction product.  This background makes it difficult to 
evaluate the presence of heterozygosity when the PCR products differ in size by 
only 2 or 4 bases.  Does anyone out there know the cause of this and, more 
importantly, how to overcome it?  Possible causes that I can imagine include 
polymerase slippage along the stretch of dinucleotide repeat or the infamous Taq
extendase activity.  Thanks for any responses!


Jack H. Lichy
AFIP Molecular Diagnostics Laboratory
Armed Forces Institute of Pathology
Washington, D.C.