A new Taq I polymorphism in Alu repeat 4 of the human factor IX gene is reported. This polymorphism is associated with a C-T transition at the 72-bp position of the Alu repeat consensus sequence. A simple PCR system for testing of this structural anomaly, with internal control of restriction hydrolysis, was developed. The frequency of the new polymorphic site and its linkage with other polymorphisms of the factor IX gene were also evaluated. The new polymorphism was used for establishing hemophilia B carriers.
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