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PubMed1991

The Xmn I site (-158, C----T) 5' to the G gamma gene: correlation with the Senegalese haplotype and G gamma globin expression.

There are three major African haplotypes associated with the sickle mutation: Benin (#19), Senegalese (#3), and Central African Republic (#20). Previous studies have suggested that the Xmn I site (-158 bp 5' to the G gamma gene) is associated with elevated levels of G gamma and with the Senegalese haplotype, while other investigators questioned this association. In order to clarify the issue, we have determined beta haplotypes, tested for the presence of the Xmn I site, and measured Hb F and G gamma expression levels in 143 American Black patients with sickle cell anemia. Haplotypes were determined using eight polymorphic sites in the beta-like globin gene cluster: Hinc II 5' to epsilon, Hind III in IVS-II G gamma and A gamma, Hinc II within and 3' to psi beta, Ava II in IVS-II of beta, and Hpa I and Bam HI 3' to beta. The G gamma /A gamma ratio was analyzed by high performance liquid chromatography using a C18 column. The Xmn I site was present in all 31 chromosomes with the Sengalese haplotype. Of the remaining 255 chromosomes with other haplotypes, only 2 (0.8%) had the Xmn I site present. There was significant correlation between the presence of the Xmn I site and increased G gamma /A gamma ratio in a dose-dependent manner. The Hb F level was not significantly increased in the presence of the Xmn I site. The data indicate that the Xmn I site maintains a G gamma /A gamma ratio typical of fetal life but does not necessarily cause elevation of Hb F. The latter seems to depend on factors other than the Xmn I site.

Adolescent↗

PubMed2000

Fine mapping of IGAD1 in IgA deficiency and common variable immunodeficiency: identification and characterization of haplotypes shared by affected members of 101 multiple-case families.

To limit the region containing a mutation predisposing to selective IgA deficiency (IgAD) and common variable immunodeficiency (CVID), 554 informative members of 101 multiple-case families were haplotyped at the IGAD1 candidate locus in the MHC. Microsatellite markers were placed onto the physical map of IGAD1 to establish their order and permit rapid haplotype analyses. Linkage analysis of this extended family set provided additional support for a strong susceptibility locus at IGAD1 with a maximum multipoint nonparametric linkage score in excess of 3. Although the transmission of maternal IGAD1 haplotypes from unaffected heterozygous parents to the affected offspring was in excess, this was not apparent in multiple-case families with a predominance of affected mothers, suggesting that this parental bias is influenced by the affection status of transmitting parents and supporting a maternal effect in disease susceptibility. Of 110 haplotypes shared by 258 affected family members, a single haplotype (H1) was found in 44 pairs of affected relatives, accounting for the majority of the IGAD1 contribution to the development of IgAD/CVID in our families. The H1 allelic variability was higher in the telomeric part of the class III region than in the distal part of the class II region in both single- and multiple-case families. Incomplete H1 haplotypes had most variant alleles in the telomeric part of the analyzed region in homozygous IgAD/CVID patients, whereas this was not observed in unaffected homozygotes. These data suggest that a telomeric part of the class II region or centromeric part of the class III region is the most likely location of IGAD1.

Alleles↗

PubMed2002

A 320-kilobase artificial chromosome encoding the human HLA DR3-DQ2 MHC haplotype confers HLA restriction in transgenic mice.

MHC class II haplotypes control the specificity of Th immune responses and susceptibility to many autoimmune diseases. Understanding the role of HLA class II haplotypes in immunity is hampered by the lack of animal models expressing these genes as authentic cis-haplotypes. In this study we describe transgenic expression of the autoimmune prone HLA DR3-DQ2 haplotype from a yeast artificial chromosome (YAC) containing an intact similar320-kb region from HLA DRA to DQB2. In YAC-transgenic mice HLA DR and DQ gene products were expressed on B cells, macrophages, and dendritic cells, but not on T cells indicating cell-specific regulation. Positive selection of the CD4 compartment by human class II molecules was 67% efficient in YAC-homozygous mice lacking endogenous class II molecules (Abeta(null/null)) and expressing only murine CD4. A broad range of TCR Vbeta families was used in the peripheral T cell repertoire, which was also purged of Vbeta5-, Vbeta11-, and Vbeta12-bearing T cells by endogenous mouse mammary tumor virus-encoded superantigens. Expression of the HLA DR3-DQ2 haplotype on the Abeta(null/null) background was associated with normal CD8-dependent clearance of virus from influenza-infected mice and development of CD4-dependent protection from otherwise lethal infection with Salmonella typhimurium. HLA DR- and DQ-restricted T cell responses were also elicited following immunization with known T cell determinants presented by these molecules. These findings demonstrate the potential for human MHC class II haplotypes to function efficiently in transgenic mice and should provide valuable tools for developing humanized models of MHC-associated autoimmune diseases.

Amino Acid Sequence↗

PubMed1999

Y-chromosome DNA haplotype 15 in Europe.

Haplotype 15 at 1 Y-chromosome-specific DNA polymorphism (p49/TaqI) was reported in a meta-analysis concerning 2418 males originating from 28 different geographic locations in Western Europe. The highest frequency of haplotype 15 (72.2%) was observed in French Basques, and it was previously deduced that this haplotype is the ancestral haplotype in Europe (Lucotte and Hazout 1996). Percentages of haplotype 15 geographic distribution show another high frequency in northwestern Europeans and a gradient of decreasing frequencies toward southeastern and peripheral countries. These results suggest that frequencies of haplotype 15 of the Y chromosome are useful to study the contribution of pre-Neolithic males to the present-day populations of Europe.

DNA, Mitochondrial↗

PubMedDate not supplied

HLA class I haplotypes in families of children with coeliac disease.

The purpose of the study was the analysis of HLA-AB haplotypes frequency in the families of children with coeliac disease. Haplotypes present in 46 probands' families including 69 affected children, 49 healthy siblings and 91 parents were verified. HLA antigens were typed by Terasaki and McClelland's routine two-step-microcytotoxic assay in NIH modification. Among 138 haplotypes, the following were significantly more frequent in affected children: HLA-A1-B8 (3116 x 10(4)), HLA-A3-B8 (290 x 10(4)) and HLA-A2-B8 (217 x 10(4)). Total frequency of haplotypes including HLA-B8 antigen in comparison to control population equalled 3986 x 10(4) vs. 763 x 10(4). HLA-A1-B8 haplotype frequency was twice lower in probands' healthy siblings and parents, equalling 1837 x 10(4) and 1868 x 10(4), respectively. Highly significantly more frequent HLA-A1-B8 haplotype found in probands' families may indicate the correlation between inherited gene products and increased risk of coeliac disease incidence.

Case-Control Studies↗

PubMed2002

HLA class II haplotypic association and DQCAR microsatellite polymorphisms in Croatian patients with psoriasis.

The purpose of the present study was to investigate polymorphism of HLA class II haplotypic associations (HLA-DRB1, -DQA1, -DQB1) and DQCAR alleles in 78 Croatian patients with psoriasis. Patients were divided into two groups according to a family history of disease and age of onset: type I (positive family history and early onset) and type II (negative family history and late onset). The difference in frequency of HLA class II haplotypic associations between type I patients and controls was observed for the following combinations: HLA-DRB1*0701, -DQA1*0201, -DQB1*02 (23.6% vs. 7.2%; p < 0.001), HLA-DRB1*0701, -DQA1*0201, -DQB1*0303 (8.5% vs. 1.3%; p = 0.0018) and HLA-DRB1*1601, -DQA1*0102, -DQB1*0502 (2.8% vs. 9.3%; p = 0.06). The difference between type II psoriasis and controls for association: HLA-DRB1*1501, -DQA1*0102, -DQB1*0602 is not significant (20.0% vs. 8.9%; p = 0.06). The significantly higher frequency of DQCAR 113bp and 119bp alleles in patients with type Ipsoriasis is a result of linkage disequlibrium of these alleles with both HLA-DRB1*0701 haplotypic associations. Analysis ofDQCAR alleles in the HLA-DRB1*0701 haplotypic associations in patients with psoriasis vulgaris and matched controls did not reveal any difference in polymorphism of DQCAR alleles. These data suggest that HLA-DRB*0701 haplotypic combinations are associated with type I but not for type II psoriasis in the Croatian population. DQCAR polymorphism is not useful genetic marker to distinguish susceptible HLA class II haplotypic association.

Adult↗

PubMed2003

Interleukin-6 promoter haplotypes and interleukin-6 cytokine responses.

Genetic variations contribute to differences in the inflammatory response and are markers for disease risk and outcomes. We studied three single-nucleotide polymorphisms (-597 G-->A, -572 G-->C, and -174 G-->C) in the IL-6 promoter to determine associations with ex vivo LPS-stimulated IL-6 production by leukocytes. We also measured nuclear protein binding to synthetic oligonucleotides representing the -174 polymorphic region, located in proximity to important transcription factor motifs. We determined genotypes at three sites in the IL-6 promoter by pyrosequencing of genomic DNA obtained from 49 healthy control subjects. To determine molecular haplotypes, cloned DNA fragments from heterozygous subjects were sequenced. IL-6 release by whole blood leukocytes was measured after 24 h of ex vivo LPS stimulation. We compared IL-6 concentrations between haplotypes using Kruskall-Wallis and adjusted for covariates by analysis of covariance. Electromobility gel shift assay was carried out by the incubation of nuclear proteins from cultured human mononuclear cells with oligonucleotides representing the alternate -174 alleles. The amount of nuclear protein binding was quantified by densitometry, which was compared using analysis of variance. Genotype and sequence analysis of genomic and cloned DNA characterized three haplotypes. Ex vivo IL-6 production was greatest in individuals who were homozygous for the haplotype containing guanine at -597 and -174. IL-6 production was least for individuals homozygous for the haplotype containing adenine at -597 and cytosine at -174. Nuclear protein bound more avidly to guanine-containing oligonucleotides representing the -174 position than to oligonucleotides containing cytosine at that position. The IL-6 promoter haplotype influences ex vivo IL-6 response to endotoxin. This effect may be due to a functional effect of the -174 G-->C polymorphism.

Adult↗

PubMedDate not supplied

[Analysis of mitochondrial DNA haplotypes in yakut population].

To study the mitochondrial gene pool structure in Yakuts, polymorphism of mtDNA hypervariable segment I (16,024-16,390) was analyzed in 191 people sampled from the indigenous population of the Sakha Republic. In total, 67 haplotypes of 14 haplogroups were detected. Most (91.6%) haplotypes belonged to haplogroups A, B, C, D, F, G, M*, and Y, which are specific for East Eurasian ethnic groups; 8.4% haplotypes represented Caucasian haplogroups H, HV1, J, T, U, and W. A high frequency of mtDNA types belonging to Asian supercluster M was peculiar for Yakuts: mtDNA types belonging to haplogroup C, D, or G and undifferentiated mtDNA types of haplogroup M (M*) accounted for 81% of all haplotypes. The highest diversity was observed for haplogroups C and D, which comprised respectively 22 (44%) and 18 (30%) haplotypes. Yakuts showed the lowest genetic diversity (H = 0.964) among all Turkic ethnic groups. Phylogenetic analysis testified to a common genetic substrate of Yakuts, Mongols, and Central Asian (Kazakh, Kyrgyz, Uigur) populations. Yakuts proved to share 21 (55.5%) mtDNA haplogroups with the Central Asian ethnic groups and Mongols. Comparisons with modern paleo-Asian populations (Chukcha, Itelmen, Koryaks) revealed three (8.9%) haplotypes common for Yakuts and Koryaks. The results of mtDNA analysis disagree with the hypothesis of an appreciable paleo-Asian contribution to the modern Yakut gene pool.

Asia, Central↗

PubMed2003

[Genetic polymorphism and the population difference of 7 Y-STR loci and haplotypes in Chinese Han and Japanese populations].

OBJECTIVE: To investigate the genetic polymorphism of 7 Y-STR loci and haplotypes and analyze their population difference. METHODS: The DNA samples from 45 Chinese Han and 59 Japanese men were analyzed by PCR and the denatured PAGE followed by silver staining. RESULTS: 33 alleles were identified for 6 loci including DYS393, DYS389 I, DYS19, DYS390, DYS389 II and DYS392, 39 alleles were identified for DYS 385, the frequency distributions were between 0.0169-0.6444, the DP value distributions of them were between 0.5406-0.9579, the DP value of DYS 385 was the highest. With the comparison of data of the 7 loci, significant difference in genetics was observed between the two populations(P < 0.05). There were 95 haplotypes that consisted of the 7 loci, Chinese Han had 41 haplotypes, DP value 0.9960, Japanese population had 54 haplotypes, DP value 0.9965, no common haplotypes were found between them. CONCLUSION: The 7 STR loci above belong to loci of high discriminating ability, the haplotypes are highly polymorphic and their ethical character is apparent.

Asian People↗

PubMed1992

Conserved, extended MHC haplotypes.

Extended major histocompatibility complex (MHC) haplotypes are fixed conserved regions of the short arm of the sixth human chromosome defined by their HLA-B, complotype (BF, C2, C4A, C4B), HLA-DR alleles. The regions of conservation may extend further. At least a third of normal MHC haplotypes in Caucasians are extended, and they are largely responsible for previously observed linkage disequilibrium in the region. They are relatively population-specific. Their presence has major implications for tissue transplantation, and particularly for the identification of unrelated donor-recipient pairs, since matching for extended haplotypes probably optimizes engraftment in individuals who have them. Even for those who do not, extended haplotypes provide the means for identifying likely MLR-I-negative donor-recipients, and for identifying the genes involved in this function. Extended haplotypes provide most of the markers for HLA-associated autoimmune diseases; like the MHCs of inbred and inbred recombinant strains of mice, they have aided in the analysis of the contribution of specific genes in this region to disease susceptibility and immune functions, particularly the antibody response. Finally, extended haplotypes must be taken into account when considering population genetic questions and when using HLA markers to identify individuals in forensic applications.

Asthma↗

PubMed2005

Mutations in the von Hippel-Lindau (VHL) tumor suppressor gene and VHL-haplotype analysis in patients with presumable congenital erythrocytosis.

BACKGROUND AND OBJECTIVES: Congenital erythrocytoses or polycythemias are rare and heterogeneous. A homozygous mutation (C598T->Arg200Trp) in the von Hippel-Lindau (VHL) gene was originally identified as the cause of the endemic Chuvash polycythemia. Subsequently this and other mutations in the VHL gene were also detected in several patients of different ethnic origin. Haplotype analyses of the VHL gene suggested a common origin for the Chuvash-type mutation. DESIGN AND METHODS: Thirty-four patients with presumable congenital erythrocytosis due to an unknown underlying disorder were examined for VHL gene mutations and VHL region haplotypes. RESULTS: Four patients were homozygous and one patient heterozygous for the Chuvash-type mutation. One additional patient presented a previously not described heterozygous mutation G311->T VHL in exon 1. The haplotype analyses were in agreement with recently published data for three of the four patients with homozygous mutations as well as for the patient with a heterozygous Chuvash-type mutation. One patient of Turkish origin with homozygous Chuvash-type mutation had a haplotype not previously found in individuals with Chuvash-type mutation. INTERPRETATION AND CONCLUSIONS: These results confirm that mutations in the VHL gene are responsible for a substantial proportion of patients with congenital erythrocytoses. Erythrocytoses due to a C598->T mutation of the VHL gene are not geographically restricted. The majority of patients with Chuvash polycythemia share a common VHL gene haplotype. The different haplotype in one of the patients with Chuvash-type mutation indicates that this mutation was not spread only from a single founder but developed independently in other individuals.

Adolescent↗

PubMed2004

Algorithms for association study design using a generalized model of haplotype conservation.

There is considerable interest in computational methods to assist in the use of genetic polymorphism data for locating disease-related genes. Haplotypes, contiguous sets of correlated variants, may provide a means of reducing the difficulty of the data analysis problems involved. The field to date has been dominated by methods based on the "haplotype block" hypothesis, which assumes discrete population-wide boundaries between conserved genetic segments, but there is strong reason to believe that haplotype blocks do not fully capture true haplotype conservation patterns. In this paper, we address the computational challenges of using a more flexible, block-free representation of haplotype structure called the "haplotype motif" model for downstream analysis problems. We develop algorithms for htSNP selection and missing data inference using this more generalized model of sequence conservation. Application to a dataset from the literature demonstrates the practical value of these block-free methods.

Algorithms↗

PubMed2006

[Analysis of polymorphisms in Y-DNA haplotypes and mtDNA haplogroups in Yao ethnic group from Guizho].

The frequencies of Y-chromosome haplotypes consisting of 12 single nucleotide polymorphisms (SNP) and mitochondrial DNA (mtDNA) haplotypes consisting of 9 SNPs were investigated using PCR-RFLP in 97 Yaos from Guizhou to study the patrilineal and matrilineal genetic structure and the origin of Yao Ethnic Group from Guizhou. Results showed that all 97 samples were classified into 4 Y-DNA haplotypes (H7, H8, H9 and H11). The major haplotype H7 of Hmong-Mien Population was highly prevalent (92.4%) in Yaos from Guizhou. Eight mtDNA haplotypes were identified through mtDNA analysis and all the haplotypes could be classified into 5 haplogroups (B4, B5, D4, D5 and N*) that were defined previously. The frequency of a 9-bp deletion in the human mtDNA Co II/tRNALys intergenic region was 58.2% in the 97 samples. These data suggest that the patrilineal genetic structure of Yao ethnic group from Guizhou was simple and Yaos from Guizhou had the typical genetic character of the Hmong-Mien Population and some admixture with other populations. The matrilineal genetic structure of Yaos from Guizhou was relatively complex and the 9-bp deletion was a characteristic genetic marker of the matrilineal genetic structure of Yaos from Guizhou.

Asian People↗

PubMed1991

The p49/TaqI Y-specific DNA haplotypes in Australian aborigines.

The TaqI/p49 Y-specific RFLPs were studied in 59 Australian aborigines. A new haplotype was found (not present in Caucasians and Africans, number XXV). In the revised genealogy of haplotypes, Australian haplotypes appear to occupy an intermediate position between African Pygmies and Papua haplotypic repartitions, while the most common Australian haplotypes (haplotype III, 25% of the subjects) is apparently derived from them.

Australia↗

PubMed2006

[Association between methylenetetrahydrofolate reductase gene haplotypes and the susceptibility of chromosomal damage in coke-oven workers].

OBJECTIVE: To investigate the association between MTHFR gene variances and chromosomal damage levels in peripheral blood lymphocyte in coke-oven workers exposed to polycyclic aromatic hydrocarbons (PAHs). METHODS: One-hundred and forty coke-oven workers who exposed to a high level of PAHs and sixty-six non-exposed controls were selected as the study subjects. Chromosomal damage in peripheral lymphocyte was measured by the cytokinesis-block micronucleus (CBMN) assay. Urinary 1-hydroxypyrene (1-OHP) levels were measured as the internal dose of PAHs exposure. Two single nucleotide polymorphisms(SNPs) in MTHFR gene, including C677T, A1298C were detected by PCR-RFLP. The MTHFR haplotypes were estimated by Bayesian statistical method with the software of PHASE Version 2.1. The associations between haplotype pairs and CBMN were assessed by analysis of covariance in the coke-oven workers and controls. RESULTS: The variant allele frequencies for MTHFRC677T and A1298C were 0.56 and 0.16 respectively, which consistent with Hardy-Weinberg equilibrium. There was linkage disequilibrium between the two SNPs (D' = 0.99) in this study. Four haplotypes were calculated by PHASE, in terms of 677T - 1298A, 677C-1298A, 677C-1298C and 677T-1298C, the frequencies were 0.555,0.279,0.163 and 0.003 respectively. In coke-oven workers, the frequencies of total micronucleus of non-677C-1298A/677C-1298A haplotype pair was significantly higher than 677C-1298A/677C-1298A (1.00 +/- 0.67 vs 0.60 +/- 0.41, P = 0.04). The frequencies of total micronucleus of 677T-1298A/677T-1298A haplotype pair was significantly higher than 677C-1298A/677C-1298A (1.08 +/- 0.71 vs 0.60 +/- 0.41, P = 0.04). In coke-oven workers, the frequencies of total micronucleus among the different SNPs were not significant differences, either in the controls. CONCLUSION: The haplotypes of MTHFR gene might be one genetic susceptibility factors of PAH induced chromosomal damage in coke-oven workers.

Air Pollutants, Occupational↗

PubMed2006

Relaxing haplotype block models for association testing.

The arrival of publicly available genome-wide variation data is creating new opportunities for reconciling model-based methods for associating genotypes and phenotypes with the complexities of real genome data. Such data is particularly valuable for testing the utility of models of conserved haplotype structure to association studies. While there is much interest in "haplotype block" models that assume population-wide regions of low diversity, there is also evidence that such models eliminate correlations potentially useful to association studies. We investigate the value of relaxing the rigidity of block models by developing an association testing method using the previously developed "haplotype motif" model, which retains the notion of representing haploid sequences as concatenations of conserved haplotypes but abandons the assumption of population-wide block boundaries. We compare the effectiveness of motif, block, and single-variant models at finding association with simulated phenotypes using real and simulated data. We conclude that the benefits of haplotype models in any form are modest, but that haplotype models in general and block-free models in particular are useful in picking up correlations near the boundaries of the detectable level.

Chromosomes, Human, Pair 22↗

PubMed1991

[Characterization of novel partial t-haplotypes tM1, tM2, tM3, tM4].

The results of genetic analysis of the effects of four novel partial mouse TM-haplotypes are presented in this work. Fertility and viability of tM/tM homozygotes and tM/t6 compounds, transmission ratio distortion (trd) in males heterozygous for tM, suppression of recombination and taillessness effects were studied. Three novel t-haplotypes tM1,2,4 are viable and heterozygous for these haplotypes males T/tM show low trd (20-30%). Comparison of these data and the t6-haplotype structure suggests that the tM1,2,4-haplotypes were derived as a result of recombination events in the non-inverted T-complex fragment located between two inversions. The tM3-haplotype is semilethal and heterozygous T/tM3 males show the trd equal to that of t6-heterozygotes. Homozygous tM3/tM3 and tM3/t6 male compounds are fertile or subfertile. Potential recombination ways of derivation of tM3 are discussed.

Animals↗

PubMed1991

The Senegal DNA haplotype is associated with the amelioration of anemia in African-American sickle cell anemia patients.

We have previously determined that in African sickle cell anemia (SS) patients three different beta-like globin gene cluster haplotypes are associated with different percent G gamma (one of the two types of non-alpha chains comprising hemoglobin F [HbF]), mean percent HbF, and percent dense cells. We report now that in adult New York SS patients, the presence of at least one chromosome with the Senegal haplotype is associated with higher Hb levels (1.2 g/dL higher) than is found for any other non-Senegal haplotype (P less than .004). The percent reticulocytes and the serum bilirubin levels were lower in these patients. When the effect of alpha-gene number was analyzed by examining a sample of SS patients with concomitant alpha-thalassemia, the same results were obtained. Because the HbF level is significantly higher among the Senegal haplotype carriers in this sample, the inhibitory effect on sickling of this Hb variant may be one of the reasons for the haplotype effect. We conclude that the Senegal beta-like globin gene cluster haplotype is associated with an amelioration of the hemolytic anemia that characterizes sickle cell disease.

Adult↗