Validity of PCR with emphasis on variable number of tandem repeat analysis

Objectives: Variable number of tandem repeat polymorphisms (VNTR) are frequently analyzed by PCR in genetic, epidemiologic and forensic studies. We wanted to explore the validity of these PCR analyses. Design and Methods: The amplification of the different alleles of the 17- and the 44-bp VNTR of the serotonin transporter gene and the 39-bp VNTR of the glycoprotein Ibα gene was analyzed. We studied the effects of the parameters magnesium, dimethylsulfoxide, 7-deaza-dGTP, formamide, betaine, PCR temperatures and different types of polymerases. Results: In all three VNTR polymorphisms selective amplification of one of the alleles of heterozygous individuals could be obtained by change of the magnesium concentration. This problem could be minimized by a combination of Taq- and Pwo-polymerases and by use of 7-deaza-dGTP. Conclusion: PCR analysis of all of these VNTRs may give reproducibly wrong results in truly heterozygous subjects due to selective amplification of only one of the alleles.