New highly polymorphic microsatellite marker in linkage disequilibrium with HLA-B

The difficulty of molecular typing of the HLA class I genes and the relevance of the genes of this region to disease susceptibility and transplantation have provided an impetus to develop useful typing markers. We have characterized by polymerase chain reaction analysis a new highly informative CA repeat localized approximately 25-kb centromeric to the gene HLA-B and 10-kb telomeric to the gene MICA. Twelve alleles defined by length were found in a sample of French Basques, with the PIC being 0.82. A detailed haplotype analysis was performed to investigate the association between this microsatellite and two others markers of the region (HLA-B gene and TNF region microsatellite). The 10 haplotypes with the highest estimated frequencies show evidence of a gametic association or linkage disequilibrium. A very strong association between the expressed HLA-B polymorphism and microsatellite alleles was also revealed in this sample and confirmed in the workshop cells lines of the Fourth Asia-Oceania Histocompatibility Workshop. This marker can be used in the fine mapping of this region and the association with some alleles of HLA-B may allow the replacement of HLA-B typing at least in a preliminary study. Moreover, these studies support the hypothesis of a high mutability for large alleles in microsatellite loci.     

Diversity of MICA and linkage disequilibrium with HLA-B in two North American populations

The MICA gene has a high degree of polymorphism. Allelic variation of MICA may influence binding of these ligands to the NK cell receptor NKG2D and may affect organ transplantation and/or disease pathogenesis. Knowledge of the population distribution of MICA alleles and their linkage disequilibrium (LD) with class I human leukocyte antigen (HLA) will enhance our understanding of the potential functional significance of the MICA polymorphism. In the present study, we characterized the MICA and HLA-B polymorphisms in two North American populations: European and African. The individual racial groups showed rather limited variation at the MICA locus, where the same set of three most common alleles, MICA*00201, *004, and *00801, account for 64 and 71% of the allele frequency in European-Americans and African-Americans, respectively. Other common alleles (allele frequency >5% in a population) include MICA*00901 and *010. MICA alleles showed strong linkage disequilibrium with HLA-B. Typically, a common MICA allele has strong LD with several HLA-B alleles, whereas most HLA-B alleles and their related serological groups are associated with a single MICA allele. The lack of evidence for an active diversification of the MICA gene after racial separation indicates an evolutionary history distinct from that of the classical HLA genes.     

A T cell clone defining a common DP/DR determinant in strong linkage disequilibrium with HLA-A9

Clone F-7 was generated by limiting dilution of lymphocytes stimulated by allogeneic PBL on MLC. Priming against the A23, Cw6, B45, DR7, DRw53, DQw2 haplotype was performed between two HLA haploidentical first degree relatives. The clone was tested for its ability to proliferate in response to a panel of 38 homozygous B lymphoblastoid cell lines plus three local T cell lines. It showed a pattern of reactivity corresponding to HLA-A9 specificity (r = 1) and presented a concomitant cytotoxic activity. Phenotypically, this clone consisted entirely of CD4 cells, as determined by indirect immunofluorescence. Its reactivity was completely blocked by anti-DR (GSP4.1, PL8, L243) and anti-DP (B7/21, PL15) Mo-Abs, whereas anti-DQ (1A3, TU22) and anti-class I (w6/32, BB7.7) Mo-Abs and anti-A9 antibodies did not inhibit its reactivity. These results may suggest that clone F-7 could recognize a DP specificity sharing common determinants with DR, which occurs in linkage disequilibrium with HLA-A9.     

HLA-A3, B7 linkage disequilibrium in hemochromatotic patients with or without insulin dependent diabetes

Sixty-six idiopathic hemochromatotic French patients were HLA-A, B typed. The previously known strong association with A3 was confirmed (RR = 10.6, P <10–⁹) and our results indicate clearly that a gene implicated in idiopathic hemochromatosis (IH) determinism is located in the HLA-A region.
The linkage disequilibrium between A3 and B7 was found to be far greater in IH patients than in controls. The authors have therefore hypothesized that this might be due to a selective advantage of this haplotype in IH. The A3, B7, Dw2 HLA haplotype has been shown to exert a protective effect against common insulin dependent diabetes (IDD). Thus the patients were divided into two groups according to the presence or absence of a definite IDD. B7 was found more frequently in IH patients without IDD but the difference is not significant.
In this context, the strong linkage disequilibrium between A3 and B7 might be due to the protective effect of the B region of this haplotype against IH secondary IDD.     

643例中国北方汉族急性淋巴细胞白血病患者人类白细胞抗原连锁不平衡分析

目的 分析643例中国北方汉族急性淋巴细胞白血病(acute lymphoblastic leukemia,ALL)患者组和20359名健康对照组的人类白细胞抗原(human leukocyte antigen,HLA)HLA-A-B、B-DR和AB-DR单倍型频率及连锁不平衡分布差异.方法 应用最大似然性算法(expectation-maximization,EM)计算患者组和对照组的HLA-A-B、B-DRB1和A-B-DRB1单倍型频率及连锁不平衡参数,采用X2检验比较其分布差异.结果 HLA-A30-B13、A2-B46、A33-B58,B13-DR7、B46-DR9、B52-DR15、B58-DR17,A30-B13-DR7、A33-B58-DR17和A1-B37-DR10单倍型是两组常见、共有呈强连锁不平衡单倍型.A30-B13、A2-B46、A33-B44、B13-DR7、A30-B13-DR7和A2-1346-DR9的单倍型频率和连锁不平衡水平,患者组低于对照组,差异有统计学意义(X2＞3.84,P＜0.05).A2-B52、A2-B27、A24-B8,B60-DR9、B27-DR4、B52-DR14、B44-DR17、B27-DR12、和A11-B27-DR12的单倍型频率和连锁不平衡水平,患者组高于对照组,差异有统计学意义(X2＞3.84,P＜0.05).结论 643例北方汉族ALL患者组HLA-A-B、B-DRB1、A-B-DRB1单倍型频率分布及连锁不平衡遗传特征和对照组具有高度的同源性.患者组与对照组之间的部分HLA单倍型频率及连锁不平衡分布存在统计学差异.本研究结果 为ALL与HLA疾病相关性及HLA相合供者的寻找提供了基础数据.     

A new HLA-A*680106 allele identified in individuals with celiac disease from the Friuli area of northeast Italy

A novel human leukocyte antigen (HLA)-A*680106 antigen was identified in two Italian individuals by polymerase chain reaction sequencing-based typing.     

MICA-STR, HLA-B haplotypic diversity and linkage disequilibrium in the Hunan Han population of southern China

Major histocompatibility complex (MHC) class I chain-related gene A (MICA) is located 46 kb centromeric to HLA-B and encodes a stress-inducible protein. MICA allelic variation is thought to be associated with disease susceptibility and immune response to transplants. This study was aimed to investigate the haplotypic diversity and linkage disequilibrium between human leukocyte antigen (HLA)-B and (GCT)(n) short tandem repeat in exon 5 of MICA gene (MICA-STR) in a southern Chinese Han population. Fifty-eight randomly selected nuclear families with 183 members including 85 unrelated parental samples were collected in Hunan province, southern China. HLA-B generic typing was performed by polymerase chain reaction-sequence-specific priming (PCR-SSP), and samples showing novel HLA-B-MICA-STR linkage were further typed for HLA-B allelic variation by high-resolution PCR-SSP. MICA-STR allelic variation and MICA gene deletion (MICA*Del) were detected by fluorescent PCR-size sequencing and PCR-SSP. Haplotype was determined through family segregation analysis. Statistical analysis was applied to the data of the 85 unrelated parental samples. Nineteen HLA-B specificities and seven MICA-STR allelic variants were observed in 85 unrelated parental samples, the most predominant of which were HLA-B*46, -B60, -B*13, and -B*15, and MICA*A5, MICA*A5.1 and MICA*A4, respectively. Genotype distributions of HLA-B, MICA-STR loci were consistent with Hardy-Weinberg proportions. The HLA-B-MICA-STR haplotypic phases of all 85 unrelated parental samples were unambiguously assigned, which contained 30 kinds of HLA-B, MICA-STR haplotypic combinations, nine of them have not been reported in the literature. Significant positive linkage disequilibria between certain HLA-B and MICA-STR alleles, including HLA-B*13 and MICA*A4, HLA-B*38 and MICA*A9, HLA-B*58 and MICA*A9, HLA-B*46 and MICA*A5, HLA-B*51 and MICA*A6, HLA-B*52 and MICA*A6, and HLA-B60 and MICA*A5.1, were observed. HLA-B*48 was linked to MICA*A5, MICA*A5.1 and MICA*Del. HLA-B*5801-MICA*A10 linkage was found in a family. Our data indicated a high degree of haplotypic diversity and strong linkage disequilibrium between MICA-STR and HLA-B in a southern Chinese Han population, the data will inform future studies on anthropology, donor-recipient HLA matching in clinical transplantation and HLA-linked disease association.     

Molecular analysis of HLA-A02 subtype frequencies in the population of Northern Italy

HLA-A^*02 is the most heterogenous HLA-A allele with seventeen molecular subtypes described so far. We have refined existing protocols for PCR-SSOP typing of these alleles by use of a single 1.6 Kb PCR-amplificate spanning the entire exons 2 and 3 as well as most of exon 4 of HLA-A^*02 genes. This allows direct screening for the presence of A^*0209 and A^*0215N, the only HLA-A^*02 subtypes with nucleotide substitutions in exon 4, without the need for two separate amplifications. A panel of twenty-four SSOPs was used to unequivocally discriminate all so far known A^*02 subtypes.

In order to assess the A^*02 subtype frequencies in the population of Northern Italy, a total of 101 HLA-A^*02 genes found in 92 healthy individuals from the Italian bone marrow registry have been analyzed so far. All these individuals were of Northern Italian origin. A total of 91 A^*02 genes typed as A^*0201 (90%) while six genes turned out to be A^*0205 (6%). A single allele typing as A^*0206, A^*0208, A^*0209 and A^*0217, respectively, was found (1% each). These data indicate that, while A^*0201 is by far the dominant A^*02 subtype in the population of Northern Italy, some rare A^*02 subtypes so far described only in ethnic groups other than Caucasians can occasionally be found. These findings suggest that molecular typing will redefine HLA-A^*02 subtype frequencies and may prove useful for optimal matching of HLA-A^*02⁺ donor-recipient pairs in unrelated bone marrow transplantation. They may also have implications on the selection of candidate patients for vaccination with HLA-A^*02 restricted peptide vaccines.     

Mixed lymphocyte reactions for individuals with phenotypic identity for specific HLA-B,DR determinants: The role of linkage disequilibrium and of specific DR and other class II determinants

Although many patients who might benefit from therapeutic bone marrow transplantation lack HLA identical sibling donors, results from many centers now indicate that transplants involving donors other than identical siblings have been successful in a substantial number of cases. Most of these cases were selected because cells from the patient and donor were compatible in mixed lymphocyte culture. We have previously shown that the prediction of mixed lymphocyte culture nonreactivity by HLA-B,DR matching is far more successful if the matched donors shared antigen combinations known to possess significant positive linkage disequilibrium. We now also show that cells from donors with unrelated haplotypes having the specific DR determinants DR1, DR2, and DR3 are more likely than cells from donors with other haplotypes to be mutually compatible in mixed lymphocyte culture. However, even cells from donors with haplotypes with the highest levels of positive linkage disequilibrium frequently show significant mutual stimulation which can, in selected family studies, be attributed to determinants like SB that map between HLA-D/DR and GLO.     

Detection and Molecular Characterization of Mycobacterium microti Isolates in Wild Boar from Northern Italy

Approximately 23,000 hunter-harvested wild boars from the pre-Alpine area of northern Italy were examined for tuberculosis over a 9-year period (2003 to 2011). Retropharyngeal and mandibular lymph nodes from the wild boars were examined grossly, and 1,151 of the lymph nodes were analyzed in our laboratory by histology (728 samples) and culture isolation (819 samples). Mycobacterium tuberculosis complex (MTBC)-specific PCR (1,142 samples) was used for molecular-level detection in tissue samples, as was a gyrB restriction fragment length polymorphism (RFLP) assay (322 samples). Lesions compatible with tuberculosis and indistinguishable from those described in cases of Mycobacterium bovis infection had been observed since 2003. Mycobacterium microti was identified directly in 256 tissue samples by the adopted molecular approaches. However, only 26 M. microti strains were obtained by culture isolation due to the well-known difficulties in isolating this slow-growing mycobacterium. During 2006, a prevalence study was performed in two provinces of the area, and the diffusion of M. microti was calculated to be 5.8% (95% confidence intervals surrounding the estimated prevalences [CI_P95%], 3.94 to 7.68%). Over the following years (2007 to 2011), the presence of M. microti appeared to be stable. All isolates were genotyped by spoligotyping and exact tandem repeat analysis (ETR types A to F). In addition to the typical vole type (SB0118), a new spoligotype lacking the 43 spacers was found. Spoligotyping was also applied directly to tissue samples, and a geographical cluster distribution of the two spoligotypes was observed. This is the first report studying the diffusion and genetic variability of M. microti in wild boar.     

Frequencies of HLA-A and HLA-B alleles in a Mexico City mestizo sample

The aim of the present study was to evaluate the frequency of HLA-A and HLA-B antigens in a sample of the Mexico City Mestizo population. Previous similar studies were done by other authors in nonrelated individuals, while the present investigation was performed in families (parents and offspring), and therefore, a more accurate estimate of gene and haplotype frequencies was obtained. The predominant antigens in descending order are A2, A24, and A28 at the A locus, whereas B39 and B35 are at the B locus, all with gene frequencies above 0.1. As expected, the two more frequent haplotypes were A2-B16 and A2-B35 (considering main specificities), both with frequencies of 0.056. Seven of the 18 significant delta values of the haplotypes (observed vs. expected) remained significant after correcting for the number of comparisons, indicating the presence of linkage disequilibrium between the HLA-A and HLA-B regions. However, only A1-B8 and A19-B13 were found to be in disequilibrium in another Mexico City Mestizo sample which had very similar HLA-A and HLA-B allele frequencies to those in the present survey, suggesting that the biological significance of the other associations is rather doubtful. Am. J. Hum. Biol. 9:1–5 © 1997 Wiley-Liss, Inc.     

HLA-A, -B, -C,and -DRB1 genotyping of 1000 Northern Irish individuals from Belfast,Northern Ireland in the United Kingdom

One thousand individuals from Belfast, Northern Ireland were genotyped at the HLA-A, -B, -C and -DRB1 loci using sequence-specific oligonucleotide probe methods. HLA-A locus genotypes display a minor Hardy–Weinberg (HW) deviation (p = 0.0375); HLA-B, -C and -DRB1 genotypes are consistent with expected HW proportions. These genotype data are available in the Allele Frequencies Net Database under identifier AFND 1243.     

Lack of linkage disequilibrium between transforming growth factor alpha Taq I polymorphism and cleft lip with or without cleft palate in families from Northeastern Italy

Cleft lip with or without cleft palate (CL ± P) is the most frequent craniofacial malformation in different human populations and its cause is largely unknown. Several studies based on population associations have suggested that an allele mapping in the transforming growth factor alpha locus could be responsible, as a risk factor, for the development of the defect. Our investigation of the Taq I polymorphism at the transforming growth factor alpha locus, performed in 40 CL ± P families, did not find evidence for linkage disequilibrium with particular alleles. Moreover, tight linkage was excluded with the traditional LOD score method. Am. J. Med. Genet. 75:203–206, 1998. © 1998 Wiley-Liss, Inc.     

The genome-wide distribution of background linkage disequilibrium in a population isolate

Recent interest in using association studies to investigate complex traits has focused attention on understanding linkage disequilibrium (LD) in the human genome. We examined the genome-wide distribution and magnitude of such background LD (BLD) using 1036 densely spaced microsatellites, in a sample from the demographically well characterized population of the Central Valley of Costa Rica. High levels of BLD were found between linked markers several centiMorgans apart, and although BLD was significantly related to genetic distance between markers it was not spread uniformly throughout the genome. Understanding the forces governing the distribution of BLD in the genome will require similar investigations using a standard set of markers in other populations.     

HLA-A and HLA-B distribution in Toto - a vanishing sub-Himalayan tribe of India

The frequency of HLA-A and HLA-B locus alleles was studied by using polymerase chain reaction-based sequence-specific primer method in a very primitive and vanishing sub-Himalayan Indian Tribe, the Toto population of North Bengal. The Toto, a Mongoloid tribe with a population size of 1172 reside only in the Totopara of Jalpaiguri district of North Bengal. We studied 40 individuals and observed some high frequency alleles when compared to other Indian tribal, non-tribal, and major world populations. Particularly, the frequency of HLA-B14 was 32.5% in the Toto population, the highest known frequency reported in any population in the world. This indigenous tribal population may harbour novel HLA alleles and unique haplotypes which extensive HLA genotyping will help to reveal, and thus further our understanding of their genetic admixture and migration patterns.     

Assessing linkage disequilibrium in a complex genetic system. I. Overall deviation from random association

Linkage disequilibrium is an important tool both at the end stages of positional cloning studies to map genes of particular interest and in reconstruction of population histories. With advances in molecular biology, complex genetic systems involving multiple highly polymorphic markers are becoming more commonly used to study linkage disequilibrium. These systems contain much more genetic information than simple two marker systems. In this article, we introduce a measure to summarize the overall deviation from random association and propose a permutation-based estimate for this measure. The performance of the proposed estimation procedure is studied through simulations. The methods proposed in this paper are then applied to population data at the dopamine D2 receptor locus (DRD2) and at the homeobox B (HOXB) gene cluster.     

HLA-A and HLA-B allele frequencies in a mestizo population from Guadalajara, Mexico, determined by sequence-based typing

HLA-A and HLA-B genes were typed by DNA sequencing in a mestizo population from Guadalajara, Jalisco, Mexico. Thirty-seven HLA-A and 51 HLA-B alleles were observed in 103 samples. The common typical Amerindian alleles (>5%) and haplotypes (>or=2.0%) found were A*02010101, *24020101, *310102, B*350101, and *4002, and A*310102-B*4002, A*240201-B*350101, and the typical European alleles were A*010101, *29010101, B*1402, B*180101, and A*020101-B*1402, A*020101-B*510101, and A*3002-B*180101. This reflects the blending of the two main parental populations of mestizos: Amerindian and Iberian. Mexicans were found to be relatively closer to the Portuguese than to Spaniards. This proximity may indicate a larger Portuguese influence in Mexicans than previously considered. Present data contribute to the understanding of the genetic structure in Mexico.