Linkage analysis and molecular haplotyping of the dopamine D4 receptor gene promoter region.

OBJECTIVES: Polymorphic regions of the dopamine D4 receptor gene and its promoter region are in the focus of psychogenetic association studies. Besides the accurate phenotype characterization, highly reliable genotyping methods are also of outstanding importance in these works.
METHODS: DNA samples of 598 healthy unrelated Caucasian individuals were used to validate the described molecular haplotyping methods and to determine the allele, genotype and haplotype frequencies and the linkage disequilibrium between the polymorphisms of the dopamine D4 receptor promoter region.
RESULTS: We described a double genotyping system for the -521CT and -616CG polymorphisms, using a polymerase chain reaction restriction fragment length polymorphism or an allele-specific amplification. Allele and genotype frequencies of the novel -615AG single-nucleotide polymorphism are also determined (-615G=13.21%). For molecular haplotyping of the three single-nucleotide polymorphisms and a 120-bp duplication polymorphism, the allele-specific amplification was combined with restriction digestion. The results of the elaborated haplotyping methods were validated by molecular haplotyping of cloned fragments.
CONCLUSIONS: The developed methods have been arranged into an 'economic' protocol that might be extended for higher reliability with a double haplotyping ('full mode'). Despite the close proximity of these sites, only a moderate linkage was found between the -615AG and -616CG (Delta(2)=0.162), between the -616AG and -521CT (Delta(2)=0.0221) and between the -615AG and -521CT single-nucleotide polymorphisms (Delta(2)=0.0346). The 120-bp duplication was shown to be in linkage equilibrium with any of the three single-nucleotide polymorphisms. Applications of these results should accelerate psychogenetic association studies of the dopamine D4 receptor gene.