Basque Samples Research Articles

Evolution of haplotypes at CCL3L1/CCL4L1

Background CCL3L1 and CCL4L1 are chemokine genes, located on chromosome 17q12 (Figure 1). They are copy number variable genes that share 95% sequence identity with their non-copy number variable paralogues CCL3 and CCL4 [1]. The copy number (CN) of these genes varies between populations [2] and has been shown to be associated with phenotypes, such as susceptibility to HIV infection [2] and SLE [3]. A CCL3L1 pseudogene, also known as CCL3L2, is present in the CCL3L1 region. This pseudogene has sequences similar to CCL3L1 gene, but lacks exon 1 of CCL3L1. As a result, its presence might affect copy number (CN) measurement and subsequent interpretations in association studies between CCL3L1 CN and diseases [4]. The copy number of CCL3L1/CCL4L1 was measured using paralogue ratio test (PRT) in 270 HapMap samples 192 UK samples and 157 Basques samples [5]. Firstly, we examined the association between the presence of the CCL3L1 pseudogene and CCL3L1 CN in the UK samples and HapMap samples by PCR. The pseudogene was found in 52 out of 192 (27.08%) of UK samples. The presence of this pseudogene is strongly associated with higher copy number of CCL3L1/CCL4L1 (P<1 × 10) (Figure 2). The presence of the pseudogene was tested in all HapMap populations (Table 1). SNP genotyping and CCL3 microsatellite assays were then carried out to define a set of flanking markers that may predict CCL3L1/ CCL4L1 CN in UK and Basque samples. The best combination of 2 flanking SNPs, rs16972085 and rs8064426, can be used to predict the CCL3L1/CCL4L1 CN in UK and Basque samples with only 70% accuracy. Although the CCL3 microsatellite alleles are not associated with CCL3L1/CCL4L1 copy number, there is extensive allelic diversity in the microsatellite. Finally, to improve the accuracy of CCL3L1/CCL4L1 CN prediction, the CCL3L1/CCL4L1 genes were sequenced in 90 CEU samples to identify sequence variants within the copy-variable genes themselves. Analysis of CCL3L1/CCL41 haplotypes in CEU samples is underway to provide information on evolution of the CCL3L1/CCL4L1 haplotypes and the relationship between these haplotypes, flanking SNPs and the presence of the CCL3L1 pseudogene.

Personal Values and Well-Being among Europeans, Spanish Natives and Immigrants to Spain: Does the Culture Matter?

The aim of this study was to analyze the relationship between personal values and well-being. Two correlational studies are presented with the following random samples: (1) four native samples: two samples from the 2006 European Social Survey (Europe n1 = 28,375, Spain n2 = 1,321) and two Basque samples (n3 = 1,770; n4 = 820); and (2) a sample of immigrants in the Basque Country (quasirandom) (n5 = 1,171). Age range of respondents was 18–60 years. The instruments used were for measuring: (1) personal values (Schwartz’s PVQ-40 or PVQ-21), and (2) well-being (Bradburn’s PNA, Goldberg’s GHQ, and life satisfaction and perceived control items from the World Value Survey). Partial correlation analysis was applied, with PVQ scale response bias controlled. The data supported a positive association of hedonic and psychological well-being with openness to experience and individualist values, and a negative association with power and conservation or collectivist values. Satisfaction with life partially mediated the relationship between personal values and affect. The results support a universal association of healthy values with well-being.

Isolated populations as treasure troves in genetic epidemiology: the case of the Basques

The Basques are a culturally isolated population, living across the western border between France and Spain and speaking a non-Indo-European language. They show outlier allele frequencies in the ABO, RH, and HLA loci. To test whether Basques are a genetic isolate with the features that would make them good candidates in genetic association studies, we genotyped 123 SNPs in a 1-Mb region in chromosome 22 in Basque samples from France and Spain, as well as in samples from northern and southern Spain, and in three North African samples. Both Basque samples showed similar levels of heterozygosity to the other populations, and the decay of linkage disequilibrium with physical distance was not different between Basques and non-Basques. Thus, Basques do not show the genetic properties expected in population isolates.

Mitochondrial DNA haplogroup diversity in Basques: A reassessment based on HVI and HVII polymorphisms

This study provides a more complete characterization of the mitochondrial genome variability of the Basques, including data on the hypervariable segment HVII of the D-loop region, which remains relatively unknown. To that end, genomic DNA from 55 healthy men living in the Arratia Valley (Biscay province) and the Goiherri region (Guipúzcoa province) was examined by direct sequencing. Three-generation pedigree charts were compiled to ensure the collection from autochthonous individuals. The most notable findings emerging from the analysis of haplogroup composition are: (i) lack of U8a mitochondrial lineage, a rare subhaplogroup recently identified in Basques and proposed as a Paleolithic marker, (ii) low frequency of haplogroup V, which conflicts with results of earlier analyses describing high frequencies in southwestern Europe, and (iii) high frequency of haplogroup J, especially subhaplogroups J1c1 and J2a. The frequency of haplogroup J does not coincide with previous mtDNA studies in present-day Basques, but is congruent with frequencies found in prehistoric and historic Basque populations. In explaining divergence in haplogroup composition between modern Basque samples, we hypothesized spatial heterogeneity promoted by population fragmentation due to extreme limitation of dispersal opportunities during the Pleistocene glaciations. Similarities between extinct and extant Basque populations as for the high frequency of lineage J, as well as the abundance of this haplogroup in northern Spain endorse a shift in the focus of attention of mtDNA analysts. A refined dissection of haplogroup J might provide more solid evidence about the process of postglacial recolonization of Europe, and thus about the shaping of the European gene pool.

DNA‐based typing of Kell, Kidd, MNS, Dombrock, Colton, and Yt blood group systems in the French Basques

The Basques demonstrate peculiar characteristics regarding blood group systems. Although ABO, Rhesus, and Duffy have been extensively studied in this population, the distribution of other groups remains largely unknown. Therefore, we evaluated the frequency of less-explored- or still noninvestigated blood groups using DNA-based assays and interpreted these data in the view of population genetics. Polymorphisms of KEL (Kell), SLCA14A1 (Kidd), GYPA/GYPB (MNS), ART4 (Dombrock), AQP1 (Colton), and ACHE (Yt) blood group genes were determined from a sample of more than 100 autochthonous French Basques using allele-specific primer PCR (PCR-ASP) methods. Our results were compared with those previously obtained by the use of serology from both Basque and non-Basque European populations. MNS*1 and JK*1 allele frequencies were comparable with those reported from Basque samples. Conversely, the KEL*1 allele frequency differed significantly. To our knowledge, this is the first time that the other three systems are studied in the Basque population. DO*1 and CO*1 allele frequencies, being respectively 0.35 and 0.96, were significantly inferior to those published from various European populations. There were some discrepancies regarding these six blood systems when comparing molecular typing with serology. These findings may be explained by differences in either criteria for individual selection or technical assays. Nevertheless, these results constitute additional data to be included in the chapter of Basque biological anthropology.

Polymorphic Alu insertions and the genetic structure of Iberian Basques

Eight Alu sequences (ACE, TPA25, PV92, APO, FXIIIB, D1, A25 and B65) were analyzed in two samples from Navarre and Guipúzcoa provinces (Basque Country, Spain). Alu data for other European, Caucasus and North African populations were compiled from the literature for comparison purposes to assess the genetic relationships of the Basques in a broader geographic context. Results of both MDS plot and AMOVA revealed spatial heterogeneity among these three population clusters clearly defined by geography. On the contrary, no substantial genetic heterogeneity was found between the Basque samples, or between Basques and other Europeans (excluding Caucasus populations). Moreover, the genetic information obtained from Alu data conflicts with hypotheses linking the origin of Basques with populations from North Africa (Berbers) or from the Caucasus region (Georgia). In order to explain the reduced genetic heterogeneity detected by Alu insertions among Basque subpopulations, values of the Wright's F(ST )statistic were estimated for both Alu markers and a set of short tandem repeats (STRs) in terms of two geographical scales: (1) the Basque Country, (2) Europe (including Basques). In the Basque area, estimates of Wahlund's effect for both genetic markers showed no statistical difference between Basque subpopulations. However, when this analysis was performed on a European scale, F(ST) values were significantly higher for Alu insertions than for STR alleles. From these results, we suggest that the spatial heterogeneity of the Basque gene pool identified in previous polymorphism studies is relatively recent and probably caused by a differential process of genetic admixture with non-Basque neighboring populations modulated by the effect of a linguistic barrier to random mating.

Genetic polymorphisms in autochthonous Basques from Northern Navarre

This survey reports primary results of classical allele frequencies on ten protein loci in a Basque population sample from northern Navarre, the less known from an anthropological and genetic point of view than the populations of the other Basque territories of Spain. Since ancient times this has been a zone of Basque population settlement, and the Basque language (Euskera) still remains deeply rooted among its autochthonous population. A total of 122 blood samples from unrelated northern Navarrese with autochthonous ascendants to the third generation were typed for GC, HP, PI, TF, ACP1, AK1, CA2, ESD, PGD and PGM1 genetic systems. Basque surnames and birthplaces were the criteria used to define family origins. Genetic structure was analyzed on different population hierarchical levels. Northern Navarre seems to be the most genetically deviated area in comparison with other Basque groups. The highest level of differentiation is observed between Navarrese and Alava Basques whereas Guipúzcoa province, the territory adjacent to northern Navarre, presents the lowest genetic distance from the study area. Northern Navarrese show some distinguishing genetic characteristics in relation to other Basque relative samples, which include high frequencies for PI*M1 and TF*C1 and low levels of PGD*C and PGM1*2 alleles. When the genetic data reported here are analyzed jointly with GM allotypes frequencies, the results significantly reinforce the relative position of Navarrese Basques as well as the topology of the Basque cluster on genetic maps. The analysis of relationships among the genetic structures of Basque population samples leads us to ask ourselves which of them fits in best with the ancient Basque population. Classical geographers placed the tribe of the Vascones in the geographical region currently known as Navarre, so extant Navarrese Basques might be considered firm candidates to denote the anthropological and genomic distinctiveness of the ancient Basques.

Genetic polymorphism and linkage disequilibrium of the HLA-DP region in Basques from Navarre (Spain).

In this work, a sample of 116 individuals from an autochthonous Basque population (northern Navarre, Spain) was typed at the DNA level for HLA-DPA1 and HLA-DPB1 loci, with the aim of analysing the genetic polymorphism and the linkage disequilibrium (LD) of the HLA-DP region. In this Basque subpopulation, the most frequent alleles were *0103 (0.767) and *0201 (0.185) for DPA1 locus, whereas for DPB1 locus the *0401 allele was predominant (0.307). Accordingly, the most frequent haplotype was DPA1*0103-DPB1*0401 (0.300), which showed a significant LD. However, the haplotypes that most differentiated the sample of Navarre from other worldwide populations already analysed were DPA1*0105-DPB1*1901 (0.011) and DPA1*0201-DPB1*7601 (0.021), both of which showed a strong LD. Analysis of the relationships between populations based on data provided by HLA-DPA1 and HLA-DPB1 loci revealed a high genetic affinity between the Basque samples (North Navarre and Guipúzcoa), which, in turn, tend to plot separately from the remaining European populations. Gene frequency clines for DPB1*01, DPB1*04 and DPB1*11 alleles among European populations are reported for the first time. These alleles showed maximum values of F(ST) (0.033, 0.034 and 0.025, respectively). Various evolutionary forces were considered in discussing the origin of the spatial structuring of the gene frequencies: (i) gene flow, argued from the hypotheses of Post-glacial recolonization from southern Europe or the demic diffusion of farmers from the Near East into Europe, and (ii) the existence of selective pressures that could have generated genetic microdifferentiation.

Distribution of Rhesus Blood Group System in the French Basques: A Reappraisal Using the Allele-Specific Primers PCR Method

Objectives: To determine for the first time using PCR the distribution of Rhesus (Rh) blood group in French Basques and compare these results with those obtained by serology in the same sample and in the historical series from various Basque subgroups. Methods: Rh polymorphism was determined in a sample of 127 autochthonous French Basques using allele-specific primers (ASP) PCR and traditional serological technique. Statistical comparisons were performed between both techniques and with the data published from various Basque subpopulations. Results: No intra-sample discrepancies were detected between ASP-PCR and serology. A high frequency of RH Ddel exceeding 0.50, as typically described from several decades, was found here (0.511), as the peculiar frequency of cde (0.456) and cDE (0.073) haplotypes. This profile, obtained by molecular analysis, was within the range of previous historical studies in various Basque subpopulations using serological approach. The Rh polymorphism among the reviewed autochthonous Basque samples indicates a heterogeneous pattern of distribution, with individuals from the Alava province demonstrating the most atypical profile. Conclusions: Molecular biology approach using PCR confirms the peculiar pattern of Rh polymorphism which was previously defined by serology among Basques. Nevertheless, this distribution profile is not homogeneous within the Basque area.

The FMR1 CGG repeat and linked microsatellite markers in two Basque valleys

Fragile X syndrome is associated with an unstable CGG repeat sequence in the 5' untranslated region of the first exon of the FMR1 gene. The present study involved the evaluation of factors implicated in CGG repeat stability in a normal sample from two Basque valleys (Markina and Arratia), to discover whether the Basque population shows allelic diversity and to identify factors involved, by using the data in conjunction with previous findings. The study was based on a sample of 204 and 58 X chromosomes from the Markina and Arratia valleys, respectively. The CGG repeat, the AGG interspersion and two flanking microsatellite markers, FRAXAC1 and DXS548, were examined. In the Markina valley, gray zone alleles (> or =35 CGG repeats) were associated with anchoring AGGs, with the longest 3' pure CGG repeats of the valley (=15), with the 5' instability structure 9+n and with one principal fragile X FRAXAC1-DXS548 haplotype 42-50. In the Arratia valley, gray zone alleles (> or =35 CGG repeats) showed the highest frequency among the Basque samples analyzed, and were associated with anchoring AGGs, with the longest 3' pure repeats (> or =20), with the 5' instability structure 9+n and with one "normal" FRAXAC1-DXS548 haplotype 38-40 (these data from Arratia suggest the existence of a "protective" haplotype). The results showed, on the one hand, differences between Markina and Arratia in factors implicated in CGG repeat instability and, on the other hand, a great similarity between the general Basque sample from Biscay and the Markina valley.

Allele variation of DYS19 and Y-Alu insertion (YAP) polymorphisms in Basques: an insight into the peopling of Europe and the Mediterranean region.

Two Y-chromosome DNA polymorphisms, the DYS19 microsatellite and the YAP (at locus DYS287), were tested in males from two autochthonous Basque populations from France and northern Navarre (Spain). The results are compared to those obtained for the same genetic markers in 32 populations from Europe, northern Africa, and western Asia. The high predominance of the DYS19*11 (190-base-pair) allele in Basques indicates that their genetic diversity for microsatellite DYS19 is around half that observed in Europeans, North Africans, and western Asians. The Y-Alu insertion (YAP+) was not detected in the Basque samples. This study attempts to throw some light on the importance of historically recent migratory movements, the main corridors of gene flow, and demographic sizes and their variations in shaping gene frequency patterns in contemporary human populations, particularly in the Mediterranean region. Historical processes may have had more significant effects on the genetic make-up of current human populations than those of prehistoric times.

New contribution to the genetics of the Basques: heterogeneity in the esterase D subtype distribution.

A random sample of 1,491 individuals from three Basque provinces was studied for the red-cell esterase D (ESD) polymorphism by means of isoelectric focusing. The following allele frequencies were observed: Vizcaya, ESD*1 = 0.933, ESD*2 = 0.058, ESD*5 = 0.009; Guipuzcoa, ESD*1 = 0.938, ESD*2 = 0.053, ESD*5 = 0.009; and Alava, ESD*1 = 0.894, ESD*2 = 0.088, ESD*5 = 0.018. The Basques from Vizcaya and Guipuzcoa display the lowest values for allele ESD*5 of any European population studied to date. The value obtained for this allele in the Basque population of Alava is significantly higher than those found in the other two Basque samples. This, together with the fact that Basques from Alava display the lowest ESD*1 frequency of any Basque series, suggests that there are genetic differences between Basque provinces.

Some red cell enzymes and haptoglobin gene frequencies in two Basque regions and León

A study was conducted to determine the distribution of phenotypes and gene frequencies of haptoglobin, phosphoglucomutase 1, esterase D, 6-phosphogluconate dehydrogenase and three monomorphic systems SOD, sMDH and NADH DIA I. Results obtained from two Basque regions and León were compared with those from other Spanish populations. Gene frequencies observed in the León sample were similar to those obtained from the other Spanish samples. The Basque samples differed from the other Spanish populations in the gene frequencies of esterase D.