Microsatellite DNA markers from HLA region (D6S105, D6S265 and TNFa) in autochthonous Basques from Northern Navarre (Spain)

Background: The extent of the genetic polymorphism of the HLA complex is becoming well characterized in Basque population and their subpopulations. This level of knowledge mainly concerns HLA class I loci. However, Basque population surveys dealing with HLA class II genes and/or microsatellites in the HLA region are still very scarce. Aim: The population genetics of three highly polymorphic short tandem repeat (STR) loci, D6S105, D6S265 and TNFa, from HLA region has been analysed in autochthonous (indigenous) Basques from Northern Navarre (Spain). The same blood samples have been typed for HLA class II genes from DQ/DR/DP regions and some findings from that information can be found therein. Subjects and methods: Blood samples were taken from 107 unrelated autochthonous Basques from Northern Navarre. The criterion used to define Northern Navarrese identity was that of three generations of Basque surnames and birthplaces. Results: The main features observed in Navarrese Basques were the rather high frequencies of alleles D6S105*4 and D6S265*7. A novel allele has been detected at the D6S265 locus (13: 145 bp). The most frequent haplotype was D6S105*8-D6S265*4 with a highly significant linkage disequilibrium being presented. The high frequency of allele TNFa*1 in Basques is noteworthy and this characteristic is not shared by other European populations, where TNFa*1 is absent or shows negligible values. The multidimensional scaling analysis (MDS) for TNFa allele frequencies has shown a high variability among populations and that alleles TNFa*1 (F-ST = 0.0615) and TNFa*12 (F-ST = 0.0424) seem to have significant influence over the spatial population configuration. TNFa*2 showed the lowest FST value (0.0077) because of its conspicuous homogeneous distribution all over the European populations. Conclusions: Findings shown here on HLA microsatellites and their relationships with other HLA class I and class II genes in Basques can be helpful for those studies mainly addressed at detecting associations between HLA genes and diseases in the Basque area as a whole, and particularly in its autochthonous population, settled there since remote times.