Linkage analysis in haemophilia A: simultaneous genotyping of two polymorphisms of the human factor VIII gene using induced heteroduplex formation

Linkage analysis is currently the most widely used approach to genetic testing in families affected by haemophilia A. Among the polymorphisms of the factor VIII gene which can be used in such studies, a TIA polymorphism affecting a BclI restriction site in intron 18 and a G/A polymorphism in intron 7 are potentially useful. Both may be analysed by polymerase chain reaction (PCR) amplification followed by restriction endonuclease digestion and gel electrophoresis (the intron 7 polymorphism does not directly affect a restriction site but a minor sequence change in one PCR primer introduces an AlwNI site if the 'G' allele is present). We have developed a novel approach for the analysis of these two polymorphisms which uses induced heteroduplex formation to distinguish their allelic forms. Heteroduplex analysis eliminates the restriction endonuclease step and reduces the analysis for both loci to PCR followed directly by gel electrophoresis. Additionally, the new test has been designed to permit both loci to be analysed in the same PCR (multiplex heteroduplex analysis). Multiplex analysis was used to determine the allele frequencies of these polymorphisms in 105 factor VIII genes in the local (South Wales) population: BclI 'T'/BclI 'A' = 0.80/0.20 +/- 0.08 (95% confidence interval), intron 7 'G'/intron 7'A' = 0.88/0.12 +/- 0.06 (95% confidence interval). The polymorphisms were found to be in strong linkage disequilibrium, The utility of multiplex heteroduplex analysis for linkage studies in haemophilia A was demonstrated by its application to carrier status investigation for an at risk female in a haemophilia A family.