Factor IX gene haplotypes and its relevance for the indirect genetic analysis of haemophilia B in its Indian perspective

Abstract

In developing countries, especially in those with limited facilities and low budget resources, a reliable approach to carrier detection and prenatal diagnosis of haemophilia B might be based on indirect diagnostic strategies. As, the cost-effectiveness of indirect genetic analysis of haemophilia B has been little investigated so far, we here report our experience in India. Polymerase chain reaction analysis of DdeI/intron1, XmnI/intron 3 and HhaI/3' flanking region of the gene for factor IX (F9) was investigated in 68 individuals (23 haemophilia patients, 18 obligate carriers, 27 probable carriers) from 23 families of haemophilia B. Linkage disequilibrium analysis was done and haplotypes were generated employing the expectation-maximization algorithm. DdeI (+) and (-) allele frequencies were found to be 0.522 and 0.478, respectively, with the highest observed heterozygosity of 46.6% as compared to XmnI (24.4%) and HhaI (42.2%). The frequencies of haplotype III and VI, that is DdeI (+)-XmnI (-)-HhaI (-) and DdeI (-)-XmnI (-)-HhaI (-) were observed to be 0.363 and 0.257, respectively. Haplotype III was found to be the most heterogeneous that suggests its efficacy in the indirect genetic analysis of F9 gene. Linkage disequilibrium analysis revealed no association between DdeI/HhaI (D' = 0.092); however, significant but incomplete linkage disequilibrium was observed in XmnI/HhaI and DdeI/XmnI (D' = 0709, 0.515, respectively). The overall cumulative polymorphism information content of these three markers increased from about 0.33 to 0.72, which suggested the efficiency of haplotyping of these markers over individual gene analysis in the direction of carrier assessment of haemophilia B in India.