Haplotypes and diplotypes in thetryptase gene (TPSAB1 gene), a highlypolymorphic gene

Resumen

Background:TPSAB1 gene codes for tryp-tase, a serine protease stored in the secre-tion granules of mast cells. It has beendescribed that this is a polymorphic genewith several described SNPs along this.TPSAB1 gene, which encodes the alpha-tryptase and beta-tryptase, is the moststudied from the functional point of view.It has a homology of 90% with TPSB2.This high degree of homology makes difficult the real characterization of theSNPs. The aim of this study is to analyzethe TPSAB1 gene SNPs in a population ofcontrol individuals.Method:A total of 110 healthy adult indi-viduals were included in this study withnormal serum tryptase levels. DNA frag-ments were amplified by PCR and subse-quently sequenced. The haplotype analysiswas carried out by the SNPAnalyzer on-line software. EM, Clark and PseudoGibbs Sampler (PGS) algorithms wereused, EM estimates haplotype frequencieswithin the given population, Clark isappropriate for homozygous genotypesand PGS uses conditional probabilities. Inorder to confirm the haplotypic character-ization and the resulting PCR fragmentswere cloned in three representative cases.Finally, the cloned DNA fragments weresequenced.Result:Combinations of the 17 mutationsprovided four haplotype combinationsobtained by EM algorithm with a fre-quency >0.05, four with Clark algorithmand three with PGS. The most frequenthaplotype is the haplotype 2 (ACGACGATGCTCCGGGT) and being the mostcommon in the population (8.5%). In ouranalysis the diplotype combinationobtained with higher frequency is GCGACGACGCTCCGGTG/GCGACGCCACTCCGGGT with a frequency of 0.025. Cloningallow us to confirm six haplotypes and toobtain two new ones All cloned samplesprovided more than two alleles.Conclusion:Given the large number ofcombinations obtained with the employedprograms and considering that more thanone gene could be simultaneously analyzed;cloning of PCR product is needed to avoidbiased results