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Thirteen Polymorphic STR Loci in the HLA Region: can they Predict HLA Alleles in South Tunisia?.

Nadia Mahfoudh*, Adia Charfi, Lilla Gaddour, Faiza Hakim, Hafedh Makni, Arwa Kamoun

In the HLA region, several microsatellites (Msats) also called Short Tandem Repeats (STR) were mapped. Msats are not themselves functional; however, their inherent polymorphism and linkage disequilibrium (LD) with HLA loci make them a robust disease-mapping tool in understanding susceptibility to autoimmune and infectious diseases. The aims of our study were to define a set of 13 STRs were evenly distributed in the HLA, to evaluate their LD with HLA alleles; and to test Msats ability to predict HLA typing. HWE was verified for all STRs except the TNFb and D6S1666 Msats. Regarding statistical parameters, we used LD and HSH analysis to ascertain the best MSAts for HLA prediction. A marker in strong LD with an HLA locus and with a low value of HSH is the most appropriate for predicting HLA alleles. For the HLA-A1-B52-DR15 haplotype, the combination of the alleles markers D6S265 (a10), D6S2810 (a7), STR-MICA (a6) and D6S2789 (a16) was necessary for haplotype prediction. In conclusion, for prediction accuracy we found that the positive predictive value (PPV), the probability of observing the particular HLA haplotype in the presence of a particular Msats allele, was the most relevant statistical parameter.