Indirect DNA/gene diagnoses via electrophoresis--an obsolete principle?

In principle, gene defects can be investigated directly or indirectly via informative polymorphisms in their vicinity. But because many defects are not yet defined molecularly, these inherited diseases can only be diagnosed indirectly via analysis of informative family situations. Since (multiple) mutation analyses, e.g. via DNA sequencing, are time-consuming and expensive, indirect analysis may still be performed initially--particularly in diseases caused by heterogenous mutations. We focus on diagnoses of neurological and (auto)immune diseases by polymerase chain reaction and separation of the DNA fragments via gel electrophoreses. Even after gene defects have been identified, indirect analysis might be necessary, for example in Huntington's chorea. Although this genetic defect has been characterized as a trinucleotide disease, indirect DNA diagnosis is still performed in particular cases for psychological reasons. The causes of autoimmune diseases are multifactorial and the inheritance is complex, involving several genes. Genome-wide screening programs may involve indirect approaches via analyses of polymorphic microsatellites. Large parts of the immunological genome can be covered when 20 or more genes are investigated simultaneously. Thus the genetic bases of autoimmune diseases are disclosed. Microsatellites themselves could have a biological meaning. We therefore discuss also DNA/protein interactions for simple tandem repeats, the major targets for indirect gene diagnoses. Only indirect evidence exists that certain simple repeats influence genomic (in)stability. Taken together, indirect gene diagnoses supplement direct approaches in a variety of different purposes and in combination with standard electrophoresis techniques.