Schematic differences between indirect genotyping techniques. Commonly used indirect genotyping techniques: single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE) and reference strand-mediated conformation analysis (RSCA). The starting material (a) is the same for all three techniques (PCR product with for instance three different sequence variants). SSCP: after denaturation, single strands form a sequence-specific structure (b). This structure leads to differential mobility in a non-denaturing matrix and two bands per variant (c). DGGE: the sequence-specific denaturation characteristics in a chemical gradient (in the gel) lead to partial separation of strands (b). This in turn leads to differential mobility and results in a single band per variant (c). RSCA: hybridisation with a labelled reference strand produces double-strands with sequence-specific mismatches (b). These mismatches lead to differential mobility in a non-denaturing matrix (c). Note that the gel with RSCA is shown for demonstrating reasons only. See method section for more details.