Shadow bands seen when typing polymorphic dinucleotide repeats: some causes and cures

Abstract

Polymorphic dinucleotide repeats are generally typed by using the PCR to generate products that are resolved on denaturing acrylamide gels. The presence of "shadow bands" on these gels often makes it difficult to score alleles reliably. We have developed procedures that overcome many of these difficulties. Important aspects of these improved procedures include using gels containing formamide as well as urea, transferring the resolved allelic fragments to nylon membranes by capillary blotting and probing the membranes with locus-specific oligonucleotide probes.