Unfortunately, RFLP patterns that are generated by VNTR polymorphisms and by other polymorphic fragments that differ by one or only a few bases cannot be resolved by Southern analysis. Also, Southern analysis cannot determine which base is polymorphic. With polymerase chain reaction (PCR), the polymorphic site of DNA can be amplified and its size and boundaries precisely determined.

Many well-characterized polymorphic VNTR DNA sites, now numbering in the thousands, are known. The availability of polymorphic VNTR sites should improve the application of gene mapping techniques to pharmacogenetically important genes. For traits whose identification has been slowed for lack of a sufficient number of markers, these polymorphic sites should remove or reduce this limitation.

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