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PubMed1994

[Spectrum of DNA haplotypes and beta-thalassemia mutations linked with them in the Azerbaijan Republic].

Haplotyping of the beta-globin gene cluster was performed on DNA samples from 110 Azerbaidzhanian beta-thalassemic patients and their families. During this study, we found 18 different haplotypes and determined the frequency of their occurrence. Nine of these haplotypes have never been observed earlier in the studied population. One of the haplotypes was found only in beta-thalassemia alleles. Several haplotypes were associated with beta-thalassemia mutations found earlier in Azerbaidzhan.

Azerbaijan↗

PubMed1993

Polymorphic haplotypes and recombination rates at the LDL receptor gene locus in subjects with and without familial hypercholesterolemia who are from different populations.

RFLPs at the low-density lipoprotein (LDL) receptor locus for TaqI, StuI, HincII, AvaII, ApaLI (5' and 3'), PvuII, and NcoI were studied in Swiss and German families with familial hypercholesterolemia (FH). A total of 1,104 LDL receptor alleles were analyzed using Southern blotting and new PCR-based techniques for detection of the TaqI, StuI, HincII, AvaII, NcoI RFLPs. Two hundred fifty-six independent haplotypes from 368 individuals of 61 unrelated Swiss families, as well as 114 independent haplotypes from 184 subjects of 25 unrelated German families, were constructed. In 76 families, clinical diagnosis of FH was confirmed by cosegregation analysis. Of the 43 unique haplotypes consisting of seven RFLPs detected in the Swiss and Germans, only 9 were common in both population samples. Analysis of linkage disequilibrium revealed nonrandom associations between several of the investigated RFLPs. ApaLI (5'), NcoI, PvuII, TaqI, and AvaII or HincII were particularly informative (cumulative informativeness .85). Relative frequencies, heterozygosity indexes, and PICs of the RFLPs from the Swiss and Germans were compared with values calculated from reported haplotype data for Italians, Icelanders, North American Caucasians, South African Caucasians, and Japanese. Pairwise comparisons of population samples by common RFLPs demonstrated unexpected differences even between geographically adjacent populations (e.g., the Swiss and Germans). Furthermore, genetic distances from the Germans to the other Caucasians were larger than to the Japanese. An unexpected lack of correlation between linkage disequilibria and physical distances was detected for the German and Japanese data, possibly because of nonuniform recombination with excessively high rates between exon 13 and intron 15. Hence, the present study revealed a striking variety of polymorphic haplotypes and heterogeneity of RFLP frequencies and recombination rates among the seven population samples.

Base Sequence↗

PubMed1993

Familial Mediterranean fever (FMF) in Moroccan Jews: demonstration of a founder effect by extended haplotype analysis.

Familial Mediterranean fever (FMF) is an autosomal recessive disease causing attacks of fever and serositis. The FMF gene (designated "MEF") is on 16p, with the gene order 16cen-D16S80-MEF-D16S94-D16S283-D16S291-++ +16pter. Here we report the association of FMF susceptibility with alleles as D16S94, D16S283, and D16S291 among 31 non-Ashkenazi Jewish families (14 Moroccan, 17 non-Moroccan). We observed highly significant associations at D16S283 and D16S291 among the Moroccan families. For the non-Moroccans, only the allelic association at D16S94 approached statistical significance. Haplotype analysis showed that 18/25 Moroccan FMF chromosomes, versus 0/21 noncarrier chromosomes, bore a specific haplotype for D16S94-D16S283-D16S291. Among non-Moroccans this haplotype was present in 6/26 FMF chromosomes versus 1/28 controls. Both groups of families are largely descended from Jews who fled the Spanish Inquisition. The strong haplotype association seen among the Moroccans is most likely a founder effect, given the recent origin and genetic isolation of the Moroccan Jewish community. The lower haplotype frequency among non-Moroccan carriers may reflect differences both in history and in population genetics.

Alleles↗

PubMed1994

Regulation of antibody specificity to Plasmodium falciparum merozoite surface protein-1 by adjuvant and MHC haplotype.

An effective malaria vaccine must be capable of eliciting a protective immune response in individuals of diverse genetic makeup. In this report, we describe the co-regulation of immune responsiveness to growth-inhibitory Plasmodium falciparum merozoite surface protein-1 (MSP-1) epitopes by MHC-linked immune response genes and by the adjuvant used in MSP-1 vaccine formulations. When congenic mice differing in MHC haplotype were immunized with MSP-1 either in CFA or incorporated into a synthetic monophosphoryl lipid A (LA-15-PH)-liposome formulation, mice of different haplotypes produced anti-MSP-1 Abs capable of inhibiting P. falciparum growth. Mice of H-2b and H-2ja haplotypes produced Abs possessing high levels of inhibitory activity upon immunization with MSP-1 in LA-15-PH/liposomes whereas these haplotypes produced noninhibitory Abs when immunized with MSP-1 in CFA. Conversely, H-2d haplotype mice produced inhibitory Abs when immunized with MSP-1 in CFA but not when immunized with MSP-1 in LA-15-PH/liposomes. The LA-15-PH/liposome adjuvant was more effective than CFA in inducing growth-inhibitory Abs. The level of parasite growth inhibition observed for a particular mouse strain correlated with Ab titers against conserved, C-terminal MSP-1 epitopes, which appear to be important targets for Ab-mediated inhibition in mice immunized with both adjuvant formulations. Our results suggest that adjuvant formulation and MHC genes act in a reciprocal manner to control immune responsiveness to specific epitopes, and raise the possibility of manipulating genetically-controlled responsiveness to vaccine Ags by utilizing alternative adjuvants in vaccine formulations.

Adjuvants, Immunologic↗

PubMed1993

Y-chromosome-specific haplotype diversity in Ashkenazic and Sephardic Jews.

DNA samples from Ashkenazic and Sephardic Jews were studied with Y-chromosome-specific DNA probes p49f and p49a to screen for RFLPs and haplotypes. All 16 European haplotypes were found in Jews, but only 2 of them (VII and VIII) were widespread. Haplotype distributions in the two Jewish populations are similar, but haplotypes XI and XV are more frequent in the Ashkenazim and haplotypes IV and V are more frequent in the Sephardim, indicating their origins.

Adult↗

PubMedDate not supplied

Influence of B-haplotype on the relative efficacy of Marek's disease vaccines of different serotypes.

To determine if B-haplotype differentially influences vaccinal immunity to very virulent Marek's disease (MD) virus challenge, chickens of five 15.B-congenic lines were vaccinated with vaccines representing serotypes 1, 2, and 3. B-haplotype differentially influenced vaccinal immunity to very virulent MD virus challenge using vaccines of all three serotypes, and different MD vaccines were optimal for some B-haplotypes. Regarding specific haplotypes, the 15.B-congenic chickens with B2 and B13 developed less protection against MD than chickens with B15 following vaccination with all three serotypes of MD vaccine, whereas the chickens with B5 and B21 developed variable protection with different MD vaccines. Thus, for induction of maximum MD resistance, it may be necessary to select a vaccine appropriate for the predominant B-haplotypes of the chicken flock.

Animals↗

PubMed1995

Molecular pathology and haplotype analysis of Wilson disease in Mediterranean populations.

We analyzed mutations and defined the chromosomal haplotype in 127 patients and Mediterranean descent who were affected by Wilson disease (WD), 39 Sardinians, 49 Italians, 33 Turks, and 6 Albanians. Haplotypes were derived by use of the microsatellite markers D13S301, D13S296, D13S297, and D13S298, which are linked to the WD locus. There were five common haplotypes in Sardinians, three in Italians, and two in Turks, which accounted for 85%, 32%, and 30% of the WD chromosomes, respectively. We identified 16 novel mutations: 8 frameshifts, 7 missense mutations, and 1 splicing defect. In addition, we detected the previously described mutations: 2302insC, 3404delC, Arg1320ter, Gly944-Ser, and His1070Gin. Of the new mutations detected. two, the 1515insT on haplotype I and 2464delC on haplotype XVI, accounted for 6% and 13%, respectively, of the mutations in WD chromosomes in the Sardinian population. Mutations H1070Q, 2302insC, and 2533delA represented 13%, 8%, and 8%, respectively, of the mutations in WD chromosomes in other Mediterranean populations. The remaining mutations were rare and limited to one or two patients from different populations. Thus, WD results from some frequent mutations and many rare defects.

Albania↗

PubMed1996

An ancient common origin of aboriginal Australians and New Guinea highlanders is supported by alpha-globin haplotype analysis.

The origins of aboriginal Australians and their relationship with New Guineans and neighboring Southeast Asians remains controversial. We have studied the alpha-globin haplotype composition of an aboriginal tribe from central Australia, to address some of the ambiguities of previous studies. Australians have a haplotype repertoire that is shared with New Guinea highlanders, a fact that strongly supports a common origin of these two populations. Further, Australians and New Guinea highlanders have a different set of alpha haplotypes from Southeast Asians and a lower genetic diversity. This, coupled with the presence of many locally specific central Australian haplotypes, suggests that much of the original diversity was lost in a population bottleneck prior to or during the early colonization of Sahul and that subsequent recovery of diversity has been accompanied by the generation of new haplotypes. These conclusions contrast with some previous genetic studies suggesting links between Australians, coastal New Guineans, and present-day Southeast Asians. Much of this discrepancy appears to be due to more recent Southeast Asian admixture on the north coast of Australia.

Australia↗

PubMed1997

Regional distribution of cystic fibrosis-linked DNA haplotypes in Brazil: multicenter study.

The restriction fragment length polymorphism (RFLP) haplotypes of cystic fibrosis (CF) alleles vary between populations. To determine the distribution of two RFLPs (XV-2C and KM-19) that are tightly linked to the CF locus, we analyzed a white sample from five different states of Brazil. The haplotypes of 314 CF- and 237 non-CF-bearing chromosomes were uniformly distributed over the five states. The XV-2C allele and haplotype frequencies and the degree of linkage disequilibrium were determined. These were similar to values previously reported in southern European countries but different from results reported for northern and central Europe and North America. In contrast, although KM-19 allele frequencies differed between Brazilian states and European and North American countries, these frequencies were similar to values reported in black Americans. A significant proportion of Brazilian CF-bearing chromosomes had less common haplotypes, suggesting a heterogeneous distribution of CF gene mutations among Brazilians. Further studies are needed to identify the mutations affecting the Brazilian CF patients with various haplotypes.

Adolescent↗

PubMed1997

HLA class II DR-DQ amino acids and insulin-dependent diabetes mellitus: application of the haplotype method.

Insulin-dependent diabetes mellitus (IDDM) HLA class II DRB1-DQA1-DQB1 data from four populations (Norwegian, Sardinian, Mexican American, and Taiwanese) have been analyzed to detect the amino acids involved in the disease process. The combination of sites DRB1#67 and 86; DQA1#47; and DQB1#9, 26, 57, and 70 predicts the IDDM component in these four populations, when the results and criteria of the haplotype method for amino acids, developed in the companion paper in this issue of the Journal, are used. The following sites, either individually, or in various combinations, previously have been suggested as IDDM components: DRB1#57, 70, 71, and 86; DQA1#52; and DQB1#13, 45, and 57 (DQB1#13 and 45 correlates 100% with DQB1#9 and 26). We propose that DQA1#47 is a better predictor of IDDM than is the previously suggested DQA1#52, and we add DRB1#67 and DQB1#70 to the HLA DR-DQ IDDM amino acids. We do not claim to have identified all HLA DR-DQ amino acids-or highly correlated sites-involved in IDDM. The frequencies and predisposing/protective effects of the haplotypes defined by these seven sites have been compared, and the effects on IDDM are consistent across the populations. The strongest susceptible effects came from haplotypes DRB1 *0301/DQA1 *0501/ DQB1*0201 and DRB1*0401-5-7-8/DQA1*0301/ DQB1*0302. The number of strong protective haplotypes observed was larger than the number of susceptible ones; some of the predisposing haplotypes were present in only one or two populations. Although the sites under consideration do not necessarily have a functional involvement in IDDM, they should be highly associated with such sites and should prove to be useful in risk assessment.

Amino Acids↗

PubMed1997

Distribution of HLA-A, B and DR genes and haplotypes in the Irish population.

The distribution of HLA phenotypes, genes and haplotypes in the normal population is of considerable importance in, for example, disease susceptibility studies, platelet transfusion support and transplantation. HLA population genetics studies have been carried out on numerous population samples, however, no major studies have been performed on Irish Caucasoids. We have analysed the HLA-A, B and DR phenotypes of 1,910 healthy unrelated Irish blood donors recruited onto the Irish Bone Marrow Donor Panel. HLA typing was performed by a combination of serology, the polymerase chain reaction with sequence-specific primers and reverse hybridisation. We calculated Hardy-Weinberg fit, phenotype and gene frequencies and two- and three-locus haplotype frequencies, linkage disequilibrium (LD) values and their significance levels and relative LD values. Compared to many other European populations, the Irish show a high frequency of HLA-A1, B7, B8 and DR2 and a reduced frequency of HLA-A9, A30, B15 and DR4. Two- and three-locus haplotypes and the combinations of alleles in positive LD were all typical of northern European populations. However, the Irish have especially high frequencies of the common HLA-A1/B8, A2/B44, A3/B7, HLA-B8/DR3, B7/DR2, B44/DR4 and B44/DR7 haplotypes, while the frequency of other relatively common haplotypes, e.g. HLA-A2/B15, is reduced. These frequencies are of particular value for estimating the likelihood of finding bone marrow donors in patients' extended families and unrelated donor panels.

Adolescent↗

PubMed1997

Beta-globin gene haplotypes in some minor ethnic groups in Thailand.

In order to provide population genetic data of various ethnic groups in Thailand, we have determined the type of hemoglobin by electrophoresis and the beta-globin gene haplotypes by PCR followed by restriction digestion in five small ethnic groups namely hill tribes, PhuTai, Chong, Lao Song and Sakai inhabiting in the north, northeast, east, central and south of Thailand, respectively. In each group, in addition to HbA and HbA2, the HbE, the most common hemoglobinopathy in Southeast Asia was detected at 2.5%, 51.6%, 84.0%, 8.6% and 11.8%, respectively. Haplotype analysis demonstrated that in all groups the beta A-globin gene was associated with various haplotypes and beta-globin gene frameworks. However, beta E -globin gene was associated with haplotypes ((-)+(-)+ + +(-)) and ((+)-(-)-(-)+(-)) on the beta-globin gene framework 2 in all ethnic groups except in Chong people whose the beta E-globin gene was mostly linked to haplotype ((-)+(-)++(-)+) and beta-globin gene framework 3 which was commonly found among Cambodian. It appears therefore that the Chong population is more related to Cambodian than Thai.

Ethnicity↗

PubMed1995

Sickle cell anemia and beta-gene cluster haplotypes in Cuba.

We have studied 91 patients with SS genotype, 44 children and 47 adults. Excluding the Cameroon and atypical haplotypes, the distribution in the children's sample exhibited 43% Benin, 38% Bantu, and 3% Senegal. In adults, the sample exhibited 46% Benin, 30% Bantu, and 9% Senegal (chi 2: 13.511, 2 df, P = 0.001). When the whole sample of 198 chromosomes (SS, SC, and S/beta thal) is considered, we find that the beta s chromosome is linked 51% to the Benin haplotype, 41% with the Bantu, and 8% with the Senegal. After adjusting for the different frequencies of beta s in Africa, these numbers would predict the port of origin to be 16% from Atlantic West Africa, 37.3% from Central West Africa, and 46% from Bantu-speaking Africa. This is in direct contradiction with the historical record that establishes a higher percentage from Bantu-speaking Africa (55%) and a much lower percentage from Senegal (3.4%). The overall conclusions from these findings is that there is a loss of Bantu haplotypes in sickle cell syndromes in Cuba, particularly among adults, and that there is an excess of Senegal haplotype, also among adults. These differences might reflect the differential survival and severity of the sickle cell disease linked to these haplotypes.

Adolescent↗

PubMed1983

HLA-B27 haplotypes in family studies of ankylosing spondylitis.

Although HLA-B27 carries a high relative risk for development of ankylosing spondylitis (AS), most B27 positive individuals do not have spondylitis. One interpretation of this observation is that there may be 2 types of B27, 1 which carries the risk factor and 1 which does not. If this were the case, then with the help of markers closely linked to HLA-B, it might be possible to detect differences between the B27 haplotypes in AS patients and those in healthy probands. We studied 197 members of 18 families with known AS and 110 members of 19 families in which HLA-B27 was present without any known inflammatory spinal disease. HLA antigens A, B, and C and alleles of complement components C2, C4, and Factor B and glyoxalase-1 were determined in all cases. Detailed haplotypes were assigned and their associations with development of the disease were examined. We were unable to identify any distinct HLA-B27 haplotype associated with AS; 2 common haplotypes and several miscellaneous ones were found in both groups. Thinking that the development of AS might be influenced by the other, non-B27 haplotype, we analyzed this and found that there was no detectable influence. The data do not contradict the notion that B27 in whites is a single entity and is itself the susceptibility factor predisposing to the development of ankylosing spondylitis.

Adult↗

PubMed1981

Differences in the cell binding affinity of a cross-reactive monoclonal anti-Ia alloantibody in mice of different H-2 haplotypes.

The analysis of an Ia specificity was performed in several H-2 haplotypes by evaluating the affinity of the binding to mouse spleen cells of a monoclonal anti-Ia alloantibody. We used the monoclonal antibody 10-2.16 (Oi et al., Curr. Top. Microbiol. Immunol. 1978. 81: 115.) which recognizes on I-A gene products a public specificity common to several H-2 haplotypes (f, ja, k, r, s and u). One parameter of the affinity (dissociation rate constant) was determined by the kinetics of the dissociation of cellbound 125 I-labeled Fab fragments in the presence of homologous antibodies. The dissociation rate constants thus obtained were different when the antibody reacted with cells from mice bearing different haplotypes and were similar for reactions with different mouse strains bearing the same haplotype. These data strongly suggest that the Ia public determinants involved are not strictly identical in different haplotypes, and support the concept that a serological cross-reaction does not necessarily mean structural identity between public antigenic determinants.

Animals↗

PubMed1981

Studies on lung tumours. V. Susceptibility of mice to dimethylnitrosamine-induced tumour formation in relation to H-2 haplotype.

Male mice of the strain A/Sn, of its congeneic partner strain A.SW, C57BL/10ScSnA (abbreviated: B10), and of two congeneic strains on a B10 background (B10.A and B10.AKM) were investigated for their susceptibility to lung tumour induction by dimethylnitrosamine (DMN) administered either by intraperitoneal injection or in the drinking water. Strain B10 (haplotype H-2b) proved to be very resistant, whereas strains A/Sn (H-2a) and A.SW (H-2s) were highly susceptible. The introduction of the haplotypes H-2a and H-2m in the resistant strain B10 resulted in a significant increase in sensitivity towards DMN-induced lung tumour formation. Lung tumour incidences in male (B10.A x B10)F hybrids, receiving DMN in drinking water, were found to be intermediate between, and significantly different from, the incidences of identically-treated parent strains B10.A and B10. Males of back-cross (B10.A x B10) x B10 BC proved to be of low susceptibility to lung tumour formation by DMN, tumour incidence being very low and not significantly different from that observed in identically-treated B10 males. It is concluded that, at least in the model system of B10-derived congeneic strains, H-2 haplotype is one of the factors important in determining susceptibility towards DMN-induced lung tumours. Comparison of C3Hf (H-2k), C3H/Sn (H-2k) and the latter's congeneic strains C3H.B10 (H-2b) and C3H.NB (H-2p) of male mice showed that these strains were moderately susceptible to both lung tumour and hepatoma formation by DMN. Accordingly, the presence of an H-2 haplotype from a lung-tumour-resistant strain (H-2b, B10) on the background of a strain of intermediate susceptibility (C3H) does not decrease susceptibility to lung tumour formation. The results were considered in the light of the H-2 haplotype dependence of spontaneous lung tumours, and consequently attention has been paid to the histological types of the induced and spontaneous lung tumours.

Adenocarcinoma, Bronchiolo-Alveolar↗

PubMed1987

Polymorphic DNA haplotypes at the human phenylalanine hydroxylase locus and their relationship with phenylketonuria.

Eight polymorphic restriction enzyme sites at the phenylalanine hydroxylase (PAH) locus were analyzed from the parental chromosomes in 33 Danish nuclear families with at least one phenylketonuric (PKU) child. Determination of haplotypes of 66 normal chromosomes and 66 chromosomes bearing mutant allele(s) demonstrated that there are at least two haplotypes which occur predominantly on PKU chromosomes and rarely otherwise. Overall, the relative frequencies of the various haplotypes are significantly different on PKU- and normal-allele bearing chromosomes, even though there is no predominantly occurring unique haplotype which can characterize the PKU chromosomes. In addition, no significant association (linkage disequilibrium) between any single polymorphic site and the mutant allele(s) was observed. The results suggest that either the phenylketonuric mutation was very ancient so that the polymorphic sites and the mutation have reached linkage equilibrium or the mutant allele(s) are the results of multiple mutations in the phenylalanine hydroxylase gene in man. Furthermore, a crude relationship between standardized linkage disequilibria and physical map distances of the polymorphic sites indicates that there is no apparent recombination hot-spot in the human phenylalanine hydroxylase gene, since the recombination rate within the locus appears to be uniform and likely to be occurring at a rate similar to that within the HLA gene cluster. The limitations of this later analysis are discussed in view of the sampling errors of disequilibrium measure used, and the potential utility of the PAH haplotypes for prenatal diagnosis and detection of PKU carriers is established.

Alleles↗

PubMed1987

Gene organization of haplotypes expressing two different C4A allotypes.

The gene organization of C4 haplotypes expressing two different C4A allotypes with a C4B null allele (C4A3A2BQ0 and C4A3A6BQO) was studied using Southern blot analysis with cDNA probes and restriction enzymes which give C4A and C4B locus-specific restriction fragments. These haplotypes were shown to have both a C4A and a C4B locus present, suggesting that the C4B locus expresses a C4A protein. The finding of a 21-OH A and a 21-OH B gene on the C4A3A6BQO haplotype further suggests that this haplotype has the common gene organization C4A, 21-OH A, C4B, 21-OH B. A model explaining C4 null alleles on haplotypes found to have two C4 loci is presented.

Alleles↗