Allelic and haplotypic data of MHC class II Alu insertions in Ngazidja (Comoros archipelago) and insight on its historical biology.

This study aimed to analyse, for the first time, five MHC class II polymorphic Alu insertions in a population with a strong Sub-Saharan African genetic background: the Ngazidja islanders and compare its allelic and haplotypic data with Worldwide populations. The genotyping was performed in 80 individuals, using simple PCR and agarose gel electrophoresis methods. Allele and haplotype frequencies, genetic diversity, Hardy-Weinberg equilibrium deviations, normalized deviate of homozygotes and pairwise linkage disequilibrium were estimated. The phylogenetic analyses included the available population data. In Ngazidja, the MHC class II Alu insertion frequencies ranged from 0.119 for AluORF10 to 0.588 for AluDPB2. Concerning haplotypes, the most predominant were the ones with only the AluDPB2 insertion allele (AluDPB22-AluDQA21-AluDQA11-AluDRB11-AluORF101), followed by the theoretical ancestral haplotype with no Alu insertions (AluDPB21-AluDQA21-AluDQA11-AluDRB11-AluORF101) and finally the haplotype with the AluDPB2 and AluDQA1 Alu insertions (AluDPB22-AluDQA21-AluDQA12-AluDRB11-AluORF10*1) with frequencies of 19.2%, 15% and 12.9%, respectively. In the phylogenetic analyses, our results indicate that the Ngazidja people are genetically differentiated from the other populations of the analysis; we found also a new haplotype that can be probably characteristic of Sub-Saharans and finally confirm the usefulness of these markers as genetic and evolutionary tools for studying genetic variations among populations of different origins.