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.     

HLA-DQA1 polymorphism in autochthonous Basques from Navarre (Spain): genetic position within European and Mediterranean scopes

In this work, a sample of 112 individuals from an autochthonous Basque population (Northern Navarre, Spain) were typed at the DNA level for the HLA-DQA1 locus, with the aim of characterizing its polymorphism and analyzing the genetic relationships of Basque Navarrese with other Caucasian populations. Northern Navarre is a neighboring area with Guipúzcoa, a province located in the core of the Basque territory having the highest proportion of Basque-speakers. In Navarrese population, the most frequent alleles were DQA1*01 (0.375) and DQA1*02 (0.259). Frequency clines for both DQA1*0103 allele and DQA1*04* allele cluster (including DQA1*0401, DQA1*0501 and DQA1*0601) among the European and Mediterranean populations considered are reported for the first time. Furthermore, a spatial structuring previously described for DQA1*02 allele is corroborated. The information provided by the highly polymorphic HLA-DQA1 locus was stressed by using genetic distances and non-metrical multidimensional scaling (MDS). The analysis of genetic relationships among populations showed a high genetic affinity between the Basque subpopulations of Northern Navarre and Guipúzcoa, which in turn tended to plot separately from the remaining European and Mediterranean populations. In the same way, the Basques showed no clear relationship to North African populations, as postulated in several previous HLA studies. The observed genetic heterogeneity seems to be conditioned by the high frequencies of the DQA1*02 allele in Basques from Guipúzcoa and North Navarre. These two subpopulations seem to show low levels of admixture with other non-Basque neighboring populations, probably because of their deeply rooted ethnicity and the existence of a linguistic barrier to random mating.     

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.     

Polymorphisms of four microsatellite DNA markers from telomeric HLA I region (D6S1624, D6S258, M6S211 and D6S510) and their linkage disequilibrium with HLA-A in a southern Chinese Han population]

OBJECTIVE: To explore the genetic polymorphisms of four microsatellite DNA markers from telomeric HLA I region (D6S1624, D6S258, M6S211 and D6S510) and their linkage disequilibrium with HLA-A in a southern Chinese Han population residing in Hunan province. METHODS: Fluorescent PCR/Size-sequencing was carried out to analyze the polymorphisms of D6S1624, D6S258, M6S211 and D6S510 loci, and polymerase chain reaction-sequence specific priming (PCR-SSP) technique was used for HLA-A typing. RESULTS: The genotypic distributions at the 5 loci were consistent with Hardy-Weinberg equilibrium (P> 0.05). The number of allelic variants for D6S1624, D6S258, M6S211 and D6S510 loci were 10, 10, 12 and 9, respectively. Each locus had several main alleles and the dominant alleles were D6S1624-*199, D6S258-*195, M6S211-*261 and D6S510-*186. All of the 4 microsatellite markers exhibited high heterozygosity values (0.7142-0.8316) and polymorphism information content values (0.6686-0.811). No global linkage disequilibrium (LD) was detected between D6S1624 and HLA-A (P= 0.2646), or between D6S258 and HLA-A (P= 0.3481). In contrast, very significant global LD was found between M6S211 and HLA-A (P< 0.0001), and between D6S510 and HLA-A(P< 0.0001). Subsequent analysis for haplotypes with an observed frequency of > or = 3% revealed that only 2 of the 10 D6S1624-HLA-A haplotypes and 3 of the 9 D6S258-HLA-A haplotypes displayed weak or moderate LD, while 7 out of the 8 M6S211-HLA-A haplotypes, 6 among the 7 D6S510-HLA-A haplotypes were in tight LD. CONCLUSION: Authors have characterized four microsatellite DNA markers, D6S1624, D6S258, M6S211 and D6S510 in a southern Chinese Han population. Findings shown here can be helpful for those studies mainly addressing the association between HLA I sub-region and diseases. The data also provide basis for future study in forensics, HLA matching in clinical transplantation and anthropology.     

Ancestry markers from the human chromosome 6: Alu repeats from the MHC in autochthonous Basques

Polymorphic Alu insertions from the MHC class I region were analyzed in 215 autochthonous Basques from Guipuzcoa and Navarre provinces, with the aim of contributing new MHC Alu data in European ancestry populations. We also seek to assess both the genetic position of native Basques among worldwide samples and the efficiency of the MHC Alu elements as ancestry informative markers (AIMs). According to the MDS and AMOVA results, worldwide populations included in the comparative analyses were grouped in three major clusters defined by genetic ancestry (Africans, Asians and Europeans). The δ values (differences in weighted allele frequencies) among ancestry groups indicated that Alu elements within the alpha-block (AluHF, AluHJ and AluHG) showed an adequate resolving power to discriminate appropriately between some of the major ancestry groups. Alpha block Alu were also revealing of the exceptionality of Basques, as they allowed for the detection of genetic heterogeneity even between Basques and the other Iberian collection considered in the analysis (Valencia). Thus, analysis of the Alu loci within the alpha-block may represent a reliable, informative and cost-effective method to explore the ancestry, geographic origins and demographic history of human populations, which can be very helpful for studies into epidemiological, forensic or evolutionary perspectives.     

中国南方汉族人群D6S1624、D6S258、M6S211、D6S510遗传多态性及与HLA-A连锁不平衡分析

目的 研究中国南方湖南地区汉族人群HLA Ⅰ类区远着丝粒端D6S1624、D6S258、M6S211、D6S510遗传多态性及与HLA-A的连锁不平衡.方法 应用荧光聚合酶链式反应-基因分型和聚合酶链式反应-序列特异性引物技术分别检测湖南地区227份正常人群样本D6S1624、D6S258、M6S211、D6S510和HLA-A位点.结果 5个位点基因型分布均符合Hardy-Weinberg平衡(P＞0.05).在D6S1624、D6S258、M6S211和D6S510位点分别检出10、10、12、9种等位基因,各位点均有若干主要等位基因,分别以D6S1624*199、D6S258-*195、M6S211-*261、D6S510-*186最为常见.在该人群中,4个微卫星位点均具有较高的杂合度值(0.7142～0.8316)和多态性信息含量(0.6686～0.811),属高度多态性位点.D6S1624、D6S258位点与HLA-A位点之间均不存在总体连锁不平衡(P=0.2646;P=0.3481),M6S211、D6S510位点与HLA-A位点之间均存在非常显著的总体连锁不平衡(P＜0.0001;P＜0.0001).对观察频率≥3%的所有单倍型做连锁不平衡分析,显示10种D6S1624.HLA-A单倍型中,仅两种处于连锁不平衡状态;9种D6S258-HLA-A单倍型中,仅3种处于连锁不平衡;而8种M6S211-HLA-A单倍型、7种D6S510-HLA-A单倍型中,分别有7种、6种均处于连锁不平衡状态.结论 所获得的4个微卫星标记的群体遗传学数据将有助鉴定HLA Ⅰ区域内与疾病相关(如鼻咽癌)的遗传标志、法医学个体认定、人类学研究,亦将有助于评价、指导临床器官移植的组织相容性配型.     

HLA alleles in isolated populations from North Spain: origin of the Basques and the ancient Iberians

HLA-A, -B, -DRB1, -DQA1 and -DQB1 alleles have been studied in three relatively isolated populations of northern Spain from Cantabria ( Pas Valleys inhabitants or Pasiegos and Cabuernigos) and from the Basque Country (Arratia Valley inhabitants). These populations have been compared with neighbouring ones and other Mediterraneans by using neighbour-joining dendrograms and plane genetic distances.     

A linkage study with DNA markers (D4S95, D4S115, and D4S111) in Japanese Huntington disease families

Summary Attempts to isolate the Huntington disease (HD) gene based on its position have been frustrated by apparently contradictory recombination events in HD pedigrees that have predicted two non-over-lapping candidate regions: 100 kb at the telomere of the short arm of chromosome 4, and a 2.2 Mb region located internally at 4p16.3. The proximal location is also supported by the detection of a linkage disequilibrium between HD and some restriction fragment length polymorphisms (RF-LPs) at the D4S95, D4S98, and D4S127 loci. In the present study, a proximal marker D4S95 showed tight linkage to the disease locus in Japanese pedigrees (Z_max=3.31, _max=0.00), while distal markers D4S115 and D4S111 did not. Particularly, a two point linkage analysis between D4S111 and HD yielded a lod score –2.01 for =0.015. This result leads to the exclusion, as a possible region of localization of the HD gene, of more than 3 cM of the genome around D4S111 locus. At the same time our results favor aforementioned proximal location as a candidate location for the HD gene.     

Genetic variation at 5 new autosomal short tandem repeat markers (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in a population-based sample from Maghreb region

Aim

To investigate allele distribution and genetic parameters of a population-based sample from Maghreb region.

Methods

Allele frequencies for 5 new autosomal short tandem repeat (STR) markers (D10S1248, D22S1045, D2S441, D1S1656, and D12S391) and several forensic parameters were determined for 95 unrelated individuals.

Results

The combined power of discrimination and power of exclusion for the 5 loci were high (0.9999991 and 0.9954757, respectively). Allele frequencies were compared with previously published population data. Significant differences were found between Maghreb population and all other populations at the locus D2S441. Also, significant differences were found between the Maghreb and the African American population at the D22S1045, D1S1656, and D12S391 loci, between Maghreb and Caucasian population at the D1S1656 locus, and between Maghreb and Hispanic population at the D22S1045 locus.

Conclusions

Typing of the 5 new STR loci may provide a useful addition to the previously established sets of autosomal STRs.Short tandem repeats (STR) are widely used for forensic testing. Ordinary paternity cases are solved by commercially available multiplexes kits, however, for more difficult cases, such as complex kinship analysis, additional STRs are needed to obtain better results. Besides, as many national DNA databases are growing and a large number of comparisons are being made within and between databases, concern for possible false-positive results may arise. This increases the need to introduce additional loci. The first European Standard Set (ESS) of loci included only 7 STRs loci, but the European Network of Forensic Science Institutes and the European DNA Profiling recommended to extend the ESS loci by adopting additional 3 miniSTRs loci (D10S1248, D22S1045, D2S441) and 2 additional polymorphic loci in 2006 (D1S1656, D12S391) (1,2).These new 5 loci improve the discriminatory power of forensic analysis and, by amplifying fragments well below current average amplicon sizes, can enhance genotyping success when analyzing highly degraded DNA (3,4).In order to verify and allow their use in forensics, the usefulness of ESS STR loci, it is necessary to obtain sufficient data from different populations.     

HLA antigens and non-HLA chromosome 6 markers in Micronesians from Nauru

HLA-A, B, C and DR antigen distributions, together with non-HLA chromosome 6 markers C2, BF, C4A, C4B and GLO, were determined in Micronesians from Nauru. Genetic distance analysis showed the close affinity between Nauruans and Filipinos, while linkage disequilibrium values confirmed some ancestral relationship between Nauru and Melanesia. HLA gene frequencies in Nauruan, Filipino and Spanish populations were used to estimate the proportionate contributions of these groups to the present day Chamorros of Guam as 36% Spanish, 17% Filipino and 47% Micronesian.     

HLA class II immunogenetics and incidence of insulin-dependent diabetes mellitus in the population of Cantabria (Northern Spain)

HLA class II genes were analyzed to study IDDM susceptibility in Cantabria (Northern Spain). Patients showed highly significant increases in DRB1*0301 (RR = 4.581, p < 0.00005), DRB1*0401 (RR = 2.6, p < 0.05), DRB1*0402 (RR = 8.78, p < 0.05) and DRB1*0405 (RR = 14.73, p < 0.005). Highly significant diferences were in the DQA1*0301 (RR = 3.62, p < 0.000005) and DQA1*0501 (RR = 2.13, p < 0.05) alleles. DQB*0201 (RR = 4.1, p < 0.00005) and DQB1*0302 (RR = 5.42, p < 0.000005) alleles were also significantly increased. A significant increase in DRB1*0402-DQA1*0301-DQB1*0302 (RR = 16.18, p < 0.05), DRB1*0405-DQA1*0301-DQB1*0302 (RR = 16.12, p < 0.05), DRB1*0301-DQA1*0501-DQB1*0201 (RR = 4.58, p < 0.00005) and DRB1*0401-DQA1*0301-DQB1*0302 (RR = 4.36, p < 0.005) was apparent in the diabetic group, while the DRB1*1501-DQA1*0102-DQB1*0602 and DRB1*1401-DQA *0104-DQB1*05031 protective haplotypes (RR = 0.17 and 0.09, p < 0.0005 and 0.05, respectively) were significantly lower in patients. The absence of Asp57 and the presence of Arg52 were associated with disease in a dose-dependent manner. Several genotypes encoding the identical DQalpha52/DQbeta57 phenotype carried very different RRs. Finally, the Cantabrian population has the highest incidence of IDDM reported for Spain (15.2 of 100.000 in the 0-14 age group, Poisson's 95% CI: 10.6-19.3).     

Significant linkage disequilibrium between the Huntington''s disease locus and markers at loci D4S10, D4S95, and D4S111 in Northern Ireland.

An analysis of the Northern Ireland Huntington's disease (HD) population of 75 families showed significant linkage disequilibrium between the HD gene and DNA markers at D4S95, D4S10, and D4S111. As the linkage disequilibrium at loci D4S10 and D4S111 is different from previous studies in the UK, but similar at locus D4S95, this suggests either that the HD mutation(s) in the Northern Ireland and British populations is not of common origin or that the haplotype of the common HD mutation has changed over time subsequent to divergence from a common origin.     

Multiple sclerosis in Gypsies from southern Spain: prevalence, mitochondrial DNA haplogroups and HLA class II association

Occasional reports have mentioned the prevalence of multiple sclerosis (MS) among Gypsies, and no studies have examined to date the prevalence of MS or human leukocyte antigen (HLA) genetics associations in the Spanish Gypsy population. We decided to study the prevalence, mitochondrial DNA (mtDNA) haplogroups and HLA class II distribution among gypsies with MS in southern Spain. We searched for Gypsy MS patients and studied HLA class II alleles by polymerase chain reaction with sequence-specific oligonucleotide (PCR/SSO) probe hybridization or sequence-specific primers amplification. An additional study of the mtDNA haplogroups by sequencing of the hypervariable segments of the control region was also performed to provide details of their ethnic origin. Estimated prevalence of MS in the Gypsy population in Malaga was 52/100,000. No significant differences were found in mtDNA between Gypsy MS patients and Gypsy controls. DRB1*1501, DQB1*0602 and DQB1*0608 alleles were the only positive HLA association with MS. The Gypsies in our series have the same anthropological origin as other European gypsy groups, as shown by mtDNA haplogroups. Although interpreted with great caution because of the small sample size, we found that the prevalence of MS in Gypsies in Malaga is not as low as that in Central Europe, although it is significantly less than that found in Caucasians from Spain (75-79/100,000). DQB1*0602 was the strongest positive association found with Gypsy MS patients, and DRB1*1501-DQB1*0602 was the most frequent haplotype in this group.     

D1S80 polymorphism,including a new variant,in a population sample from Barcelona (Spain) using polymerase chain reaction

Allele and genotype frequencies for the D1S80 (MCT118) locus have been determined in a population sample from Barcelona (Spain) using the polymerase chain reaction (PCR) amplification and nonradioactive detection. In a total of 216 unrelated individuals, 24 alleles (23 common and 1 rare variant) and 67 genotypes (64 common and 3 variants) were observed. The 216 individuals came from 162 blood samples taken for paternity studies, 16 bloodstains from forensic cases, and 38 root hairs from normal individuals. The D1S80 locus demonstrated a heterozygosity of 0.7916, and a power of discrimination of 0.9731. The distribution of genotypes is in agreement with expected values according to the Hardy-Weinberg equilibrium. Additionally, the population from Barcelona differs, significantly, from the Finnish population and also, but with lower differences, from a U.S.A. Caucasian population. © 1993 Wiley-Liss, Inc.     

HLA-A*2402 and a microsatellite (D6S248) are secondary independent susceptibility markers to ankylosing spondylitis in Basque patients

Ankylosing spondylitis (AS) is universally associated with human leukocyte antigen B27 (HLA-B27), although other genes could determine the development and clinical expression of the disease. HLA-A9 (A*2402) allele was previously found to be associated in Basque patients. The objective of this study is to perform a more precise analysis of microsatellite polymorphisms in HLA-A*2402 and B27 haplotypes to elucidate the significance of this association. A group of 50 unrelated AS patients and 113 controls of Basque origin were studied. Eight microsatellites in the class I major histocompatibility complex region with vicinity to HLA-A and -B were analyzed and the strength of allelic associations to AS and linkage disequilibrium (LD) between alleles were evaluated. Allele 15 at the microsatellite locus D6S248, 1000 Kb telomeric to HLA-A showed a strong positive association with the disease (OR:6; pc=4.7x10(-4)) and it could not be explained by LD to HLA-B27, HLA-A*2402 or any other loci. We found that D6S248-15 allele together with HLA-A*2402 could be B27-independent markers of additional susceptibility gene/s localised in the region telomeric to HLA-A in Basque AS patients.     

Y Chromosome and Mitochondrial DNA Characterization of Pasiegos, a Human Isolate from Cantabria (Spain)

Mitochondrial DNA sequences and Y chromosome haplotypes were characterized in Pasiegos, a human isolate from Cantabria, and compared with those of other Cantabrian and neighbouring Northern Spain populations. Cantabria appears to be a genetically heterogeneous community. Whereas Lebaniegos do not differ from their eastern Basque and western Asturian and Galician neighbours, Pasiegos and other non‐Lebaniego Cantabrians show significant differences with all of them. Pasiegos are peculiar for their high frequencies of Y chromosomal markers (E‐M81) with North African assignation, and Y chromosomal (R‐SRY2627) and mtDNA (V, I, U5) markers related to northern European populations. This dual geographic contribution is more in agreement with the complex demographic history of this isolate, as opposed to recent drift effects. The high incidence in Cantabrians with pre‐V and V mtDNA haplotypes, considered as a signal of Postglacial recolonization in Europe from south‐western refugees, points to such refugees as a better candidate population than Basques for this expansion. However, this does not discount a conjoint recolonization.     

青岛地区D6S477等五个短串联重复序列基因座的遗传多态性研究

目的 了解D6S477等5个基因座在青岛地区汉族群体中基因型分布及等位基因频率等遗传多态性数据，初步探讨其应用价值。方法 收集200名青岛地区汉族无关个体的静脉血，ACD抗凝，采用Chelex法提取DNA，应用聚合酶链反应技术，扩增D6S477、D9S1118、D18S865、D19S400和D20S161基因座的短串联重复序列，聚丙烯酰胺凝胶垂直电泳，银染显色分型。结果 获得了青岛地区汉族群体上述5个基因座的等位基因频率，基因型分布均符合Hardy-Weinberg平衡（P〉0．05）。结论 这5个基因座在青岛地区汉族群体中有较高的非父排除率和个人识别机率，在遗传学研究中有较高的应用价值。