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Results for “haplotype”

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At least 19 recordsLinked to original sources

PubMed1992

Haplotypes in SS patients from Nigeria; characterization of one atypical beta S haplotype no. 19 (Benin) associated with elevated HB F and high G gamma levels.

We have determined the haplotypes of 669 beta S and 109 beta A chromosomes from numerous members of 297 Nigerian families of various ethnic backgrounds. Among the beta S chromosomes, haplotype 19 was detected in 93.2%, haplotype 17 in 3.4%, and haplotype 20 in 0.1%, while 2.4% represented atypical haplotypes. As many as 60.6% of the beta A chromosomes exhibited haplotype 19 mutations, 8.2% had haplotype 3, and 1.8% had haplotype 20. Two siblings with elevated Hb F and G gamma levels were heterozygous for a beta S chromosome with haplotype 19 and a second chromosome with a hybrid haplotype (termed 19 B). In this hybrid chromosome, haplotype 3-like locus control region (LCR) [hypersensitive site-2 (HS-2)] sequences are in juxtaposition to those of the 5' flanking region of the G gamma promoter of a beta S chromosome with haplotype 19. The presence of this hybrid chromosome is associated with high G gamma values in individuals with both sickle cell anemia (SS) and sickle cell trait (AS); it closely resembles another hybrid beta S chromosome, termed 19 A, observed in a previously reported Turkish SS patient who was homozygous for this chromosome and had high Hb F and high G gamma values. In both instances, it is hypothesized that the haplotype 3-like sequences of the LCR HS-2 contain genetic determinants that can combine with factors produced during hematopoietic stress, resulting in increased gamma-globin gene expression.

Adolescent↗

PubMed1989

The DR3(w18),DQw4 haplotype differs from DR3(w17),DQw2 haplotypes at multiple class II loci.

The polymorphism of HLA class II molecules in man is particularly evident when comparisons between population groups are made. This study describes a DR3 haplotype commonly present in the American black population. Unlike the Northern European population, in which almost all DR3 individuals are DQw2, approximately 50% of DR3-positive American blacks express a DQw4 allelic product. This study characterizes the DR subregion of that haplotype. cDNA sequence analysis has revealed a DR beta gene which differs at several positions from previously described DR3 beta 1 genes. It is postulated that a gene-conversion-like event with a DRw52 beta gene as donor has generated some of these differences. The haplotype carries a DRw52a allele as defined by oligonucleotide hybridization studies. DNA restriction fragment analysis using a family and several unrelated individuals has allowed us to identify DR alpha and beta fragments associated with the DR3(w18),DQw4 haplotype. The most striking observation is that the DR3(w18),DQw4 haplotype differs from DR3(w17),DQw2 haplotypes at multiple class II loci. Several genetic mechanisms including reciprocal recombination, gene conversion, and point mutation were involved in generating the differences between these haplotypes. Once established, the DR3(w18),DQw4 haplotype appears to be relatively stable in the population.

Amino Acid Sequence↗

PubMed1992

Ancestral haplotypes: conserved population MHC haplotypes.

We describe here a number of Caucasoid MHC haplotypes that extend from HLA-B to DR and that have been conserved en bloc. These haplotypes and recombinants between any two of them account for 73% of unselected haplotypes in our Caucasoid population. The existence of ancestral haplotypes implies conservation of large chromosomal segments. Irrespective of the mechanisms involved in preservation of ancestral haplotypes, it is clear that these haplotypes carry several MHC genes, other than HLA, which may be relevant to antigen presentation, autoimmune responses, and transplantation rejection. In light of the existence of ancestral haplotypes, it is critical to evaluate MHC associations with disease and transplantation outcome in terms of associations with ancestral haplotypes rather than individual alleles.

Alleles↗

PubMed1988

The E beta hot spot of recombination in wild-derived natural recombinant MHC haplotypes. Cross-over site mapping and the identification of a 1.0-kb E beta deletion in the p and w14 haplotypes.

Detailed molecular analysis of three wild-derived MHC haplotypes provided evidence for an important role of the E beta recombinational hot spot in the recent evolution of the mouse I region. Examination of RFLP and restriction maps of cloned DNA permitted the mapping of the natural cross-over events in the haplotypes carried by strains B10.GAA37 (w21) and B10.KPB128 (w19) to a fragment of DNA not exceeding 4.1 kb, which lies almost entirely within the intron separating the beta 1 and beta 2 exons of the E beta gene. In the w14 haplotype (strain B10.STC77), which appears to be a natural recombinant between a p-like parental haplotype and another wild-derived haplotype, the site of crossing over can be mapped to a segment between the beta 2 exon of the E beta gene (left border) and the E beta 2 gene (right border). This segment containing the cross-over site in the w14 haplotype includes the E beta hot spot. In addition, the w14 haplotype as well as the standard p haplotype contain a deletion of approximately 1.0 kb in the second intron of the E beta gene, which may represent the product of an unequal cross-over event in a E beta recombinational hot spot.

Animals↗

PubMed1978

Comparison of the haplotypes of the major histocompatibility complex in the rat. III. Two difficult haplotypes: H-1h (Ag-B12) in the HW strain and Ag-B13 (H-1m) in the MNR/N strain.

Two haplotypes which posed difficult problems in serological identification, those of the HW and MNR/N strains, were studied. The HW strain was originally described as a unique haplotype (H-1h), but breeding difficulties precluded its detailed serological analysis. The red blood cells of the HW strain agglutinate weakly and cross-react with antisera to the Ag-B8 group. Anti-HW antisera cross-react strongly with LEW, ACI and WKA, but absorption with these strains did not produce an adequate typing serum. By judicious selection of recipients, however, an appropriate typing reagent could be made; a particularly useful one was (BUF X MR)F1 anti-HW absorbed with WKA red blood cells. The HW haplotype segregated appropriately in a (DA X HW)F2 population. The HW strain is a low responder to poly(Glu52Lys33Tyr15). The H-1h haplotype of this strain was designated Ag-B12. The MNR/N strain had not previously been studied serologically, although its MLR type had been defined as H-1c (MLR-5). Antisera to MNR/N cross-reacted strongly with the H-1a,b,d,f haplotypes, but MNR/N red blood cells agglutinated only weakly with many antisera. An operationally monospecific reagent antiserum to the MNR/N haplotype could not be made. The uniqueness of the MNR/N haplotype was shown by F1 tests with LEW.1A, LEW.1D and LEW.1F, by various serological analyses, including production of antisera against MNR/N and in the MR strain; by segregation studies with (LEW X LEW.1D)N5 and (DA X DA.MNR)N4 segregating back-cross populations, and by grafting skin from (DA X DA.MNR)N4 homozygous and heterozygous animals to DA recipients. The MNR/N strain is a high-responder to poly(Glu52Lys33Tyr15). The MNR/N haplotype of this strain was designated Ag-B13 (H-1m). The data led to the working hypothesis that the MNR/N strain may be a recombination between the A region of H-1d and the B region of H-1c. In addition, the H-1d private specificity at the A region was probably lost by a deletion mutation which left the main complex of public specificities intact.

Animals↗

PubMed1989

The "Sardinian" HLA-A30,B18,DR3,DQw2 haplotype constantly lacks the 21-OHA and C4B genes. Is it an ancestral haplotype without duplication?

The C4 and 21-OH loci of the class III HLA have been studied by specific DNA probes and the restriction enzyme Taq 1 in 24 unrelated Sardinian individuals selected from completely HLA-typed families. All 24 individuals had the HLA extended haplotype A30,Cw5,B18, BfF1,DR3,DRw52,DQw2, named "Sardinian" in the present paper because of its frequency of 15% in the Sardinian population. Eighteen of these were homozygous for the entire haplotype, and six were heterozygous at the A locus and blank (or homozygous) at all the other loci. In all completely homozygous cells and in four heterozygous cells at the A locus, the restriction fragments of the 21-OHA (3.2 kb) and C4B (5.8 kb or 5.4 kb) genes were absent, and the fragments of the C4A (7.0 kb) and 21-OHB (3.7 kb) genes were present. It is suggested that the "Sardinian" haplotype is an ancestral haplotype without duplication of the C4 and 21-OH genes, practically always identical in its structure, also in unrelated individuals. The diversity of this haplotype in the class III region (about 30 kb less) may be at least partially responsible for its misalignment with most haplotypes, which have duplicated C4 and 21-OH genes, and therefore also for its decreased probability to recombine. This can help explain its high stability and frequency in the Sardinian population. The same conclusion can be suggested for the Caucasian extended haplotype A1,B8,DR3 that always seems to lack the C4A and 21-OHA genes.

Blotting, Southern↗

PubMed1977

Comparison of haplotypes of the major histocompatibility complex in the rat. I. The Ag-B7 (H-1g) and Ag-B8 (H-1k) haplotypes.

Two haplotypes of the major histocompatibility complex of the rat, Ag-B7 and Ag-B8, have been compared with known H-1 haplotypes using the F1 skin-graft test and the dextran haemagglutination test. Both of these Ag-B haplotypes were different from the known H-1 haplotypes and determined different private specificities. The Ag-B7 haplotype was denoted as H-1g and the Ag-B8 haplotype as H-1k. The complex structure of the serologically detected antigenic products of these haplotypes was determined by means of H-1 congenic lines.

Alleles↗

PubMed1992

Structural similarity of the HLA-DQ region in DQ3 and DQ4 haplotypes and structural diversity of the HLA-DQ region in HLA-DR7 haplotypes.

Genomic DNA obtained from a B lymphoblastoid cell line was digested with appropriate restriction endonuclease and hybridized with several probes specific for genes encoding HLA-DQ. Southern hybridization with a DQA1 3'untranslated (UT) region probe showed DQ2-type hybridization pattern in DR7DQ3 haplotype. On the contrary, DQB1 3'UT probe showed DQ3-type pattern in the same haplotype. Gene cloning and DNA sequencing analysis revealed a repetitive sequence, (TG)19, between DQA1 and DQB1 gene in the DR7DQ3 haplotype. These results suggest that a recombination event has occurred near this potential Z-DNA structure in the haplotype, DR7DQ3. The 3'UT region probes of DQA1 and DQB1 genes failed to detect restriction fragment length polymorphism (RFLP) differences between DR4DQ3 and DR4DQ4 haplotypes in this experiment, suggesting that the gene structure between DQA1 and DQB1 is conserved in these haplotypes.

Antigenic Variation↗

PubMed1992

Ancestral haplotypes carry haplotypic and haplospecific polymorphisms of BAT1: possible relevance to autoimmune disease.

The human BAT1 gene, located in the central MHC region (approximately 170 kb centrometric of HLA-B), is polymorphic and the polymorphism correlates with MHC ancestral haplotypes. Allelic RFLP patterns have been assigned to several ancestral haplotypes and have been shown to be 'haplotypic' (i.e. found on all examples of the same ancestral haplotype) and in some cases 'haplospecific' (i.e. unique to one ancestral haplotype). The relevance of the BAT1 polymorphism to susceptibility to Myasthenia Gravis (MG) has been investigated. The frequency of the BAT1 B allelic pattern is increased in patients with MG (n = 16) compared to an equal number of control subjects. The increase is due to the association between MG and the 8.1 ancestral haplotype (HLA A1, Cw7, B8, BfS, C4AQ0, C4B1, DR3, DQw2).

Autoimmune Diseases↗

PubMed1992

Y chromosome probe p49a detects complex PvuII haplotypes and many new TaqI haplotypes in southern African populations.

Y-specific 49a/TaqI haplotypes were determined for 831 individuals drawn from 21 different southern African populations. A total of 31 new haplotypes were observed, some of which contained new alleles or allelic variants. Duplication, in addition to CpG mutation, is implicated in the generation of certain allelic variants. Cluster analysis of genetic distances between the populations, calculated using the 49a/TaqI haplotype frequencies, revealed a basic split between African and non-African populations. Hybrid groups cluster with the caucasoid groups, indicating that male gene flow has occurred from the latter into the former. Clustering of the negroid and Khoisan groups is not what might have been expected from the known linguistic affinities. It is suggested that the 49a/TaqI haplotype analysis of these populations is not sufficiently sensitive to distinguish between many of the populations. The Y-specific 49a/PvuII polymorphism was studied in 127 individuals from southern African populations, and 17 polymorphic fragments ranging in size from 3.6 kb to greater than 48 kb were identified. A total of 53 PvuII haplotypes were observed, corresponding to only 30 TaqI haplotypes. There appears to be poor correlation between the two polymorphisms.

Africa, Southern↗

PubMed1991

C4 polymorphism and major histocompatibility complex haplotypes in IgA deficiency: association with C4A null haplotypes.

IgA-deficient individuals (n = 110) and six families comprising 9 cases of IgA deficiency were typed for HLA-A, -B, -DR, C4 and factor B. Phenotype frequencies were increased for HLA-B8 (p = 0.004), HLA-DR3 (p = 0.001) and homozygous C4AQ0 (p = 0.01) and decreased for HLA-B7 (p = 0.004), HLA-DR2 (p = 0.0001) and C4A3 (p = 0.00007) compared to controls. Homozygous C4A deficiency was found in 20% of IgA-deficient persons. As clearly suggested by investigation of families, the findings could be attributed to high prevalence of the extended major histocompatibility complex (MHC) haplotype [HLA-A1, B8, C4AQ0, C4B1, BfS, DR3] in IgA deficiency. All but 1 of the 9 IgA-deficient persons included in the family study carried this haplotype and 4 of them were homozygous. In the families, 3 persons with normal serum IgA concentrations had the same MHC haplotypes as their IgA-deficient relatives. The findings were also consistent with possible overrepresentation of other MHC haplotypes with aberrant C4 gene organization in IgA deficiency. As previously suggested, the presence of two MHC haplotypes associated with IgA deficiency appears to be a necessary but not sufficient requirement for manifestation of the condition. The putative existence of a recessive gene in the MHC with regulatory function with regard to IgA gene expression is consistent with the findings.

Complement C4↗

PubMed1977

Comparison of haplotypes of the major histocompatibility complex in the rat. II. Serological analysis of the haplotypes H-1a (Ag-B4), H-1d (Ag-B9) and H-1f (Ag-B10).

The strongly cross-reacting haplotypes of the inbred strains DA, ACI, ACP, MR, BD V and AS2, and of the congenic lines LEW.1A, LEW.1D and LEW.1F, were explored. All of these inbred strains and these congenic lines type with anti-Ag-B4 antisera raised against the DA strain, which behaved as operationally mono-specific in previously reported studies of the eight currently defined Ag-B haplotypes. Serological analyses showed that this cross-reactivity was due to antibodies against public antigenic specificities which were not previously recognized as being in the anti-Ag-B4 antisera, due to the fact that the LEW.1D and LEW.1F animals were not available for testing. With the use of appropriate antisera and of absorption studies, two haplotypes in the H-1 system were found not to have been previously identified in the Ag-B system. The animals carrying the H-1d haplotype (MR, BD V and LEW.1D) have been designated as Ag-B9, and those carrying the H-1f haplotype (AS2 and LEW.1F) have been designated as Ag-B10. With the proper absorptions, an anti-Ag-B4 antiserum can be prepared which reacts only with the DA, ACI and ACP strains, and it will henceforth be used as the operationally mono-specific Ag-B4 typing reagent. A variety of typing experiments showed that the results using antisera raised in Pittsburgh and in Prague and using the Ficoll and dextran haemagglutination methods were the same.

Alleles↗

PubMed1990

Phenylketonuria mutation in Chinese haplotype 44 identical with haplotype 2 mutation in northern-European Caucasians.

DNA amplification with the polymerase chain reaction was employed to identify the phenylketonuria (PKU) mutation in Chinese PKU families. The amplified DNA was hybridized with oligonucleotides corresponding to the two most common mutant alleles, i.e., mutations associated with PKU haplotype 2 and 3 among Caucasians of northern-European ancestry. The results of analysis demonstrate that the mutation in Chinese haplotype 44 is a single-base substitution corresponding to the mutation associated with haplotype 2 in Caucasians, whereas the mutations of the phenylalanine hydroxylase gene in haplotypes 4, 7, 11 and 28 among Chinese do not correlate with either of the two mutations identified in northern-European Caucasians.

Asian People↗

PubMed1985

Haplotype study on C4 polymorphism in Japanese. Associations with MHC alleles, complotypes, and HLA-complement haplotypes.

Genetic polymorphism of the fourth component of human complement (C4) was investigated in 83 Japanese families which have been typed for HLA-A,-B,-C,-DR, C2, and BF. Four common C4A alleles and four common C4B alleles were observed. The allele frequencies estimated from unrelated parents were as follows: C4A3, 0.686; A4, 0.132; A2, 0.106; AQ0, 0.067; ARares, 0.009; C4B1, 0.587; B2, 0.167; B5, 0.088; and BQ0, 0.158. Eight different C4 haplotypes were observed with frequencies of more than 0.01. The estimated haplotype frequencies were as follows: C4A3-B1, 0.513; A4-B2, 0.114; A2-BQ0, 0.106; A3-B5, 0.088; AQ0-B1, 0.059; A3-BQ0, 0.047; A3-B2, 0.038; A4-B1, 0.015; and Rares, 0.021. Strong positive gametic associations were found in the following C4-HLA haplotypes: C4A2BQ0-A24, C4A2BQ0-Bw52, C4A3B5-Bw54, C4A3B5-Bw59, C4A4B2-Bw46, C4A3B5-Cw1, C4A2BQ0-DR2, and C4A3B5-DR4. Eleven complotypes were observed with frequencies of more than 0.01. C4A2BQ0 and C4A3B5 were exclusively associated with BFS-C2C. BFF was associated with C4A3B1. C2AT, C2B, and C2BH were associated with C4A3B1, A4B2, and C4A3B1, respectively. Eight different HLA-complement haplotypes were found to be characteristic of Japanese. These combinations are considerably different from those reported in Caucasoid populations.

Alleles↗

PubMed1979

Comparison of the haplotypes of the major histocompatibility complex in the rat. IV. The six original Ag-B haplotypes.

The six original haplotypes described in the Ag-B system were compared with their counterparts in the H-1 system. Antisera to the Ag-B haplotypes raised in inbred rats and antisera to H-1 haplotypes raised in congenic lines were tested against various panels of cell from inbred and congenic lines by the dextran and Ficoll haemagglutination methods. The private and strong public specificities detected in both systems were the same, but there were some minor differences in the intermediate and weak reactivities detected. The cross-reactivity of the antisera raised in inbred rats was broader than that of antisera raised in congenic lines. The identity of the antigenic products detected in the two systems by the dextran and Ficoll tests was further confirmed by a variety of absorption analyses and by F1 tests. This study completes the systematic serological comparison of the haplotypes of the major histocompatibility complex of the rat described originally in the Ag-B and H-1 systems.

Animals↗

PubMed1990

Frequency of the delta F508 mutation and XV2c,KM19 haplotypes in cystic fibrosis families from The Netherlands: haplotypes without delta F508 still in disequilibrium.

We have determined the frequency of the major cystic fibrosis (CF) three base pair deletion (delta F508) mutation in 152 CF chromosomes from patients originating from the northern part of The Netherlands. In these patients, the deletion represents approximately 76% of CF mutations. Meconium ileus is strongly associated with homozygosity for the delta F508 mutation. The XV2c,KM19 haplotypes on the CF chromosomes without the delta F508 mutation are in disequilibrium with the population frequency, although showing an increased frequency of the 1 2 haplotype. The surplus of this haplotype is almost entirely made up by the pancreatic insufficient patients.

Cystic Fibrosis↗

PubMed1991

Testing for haplotype sharing by siblings with incomplete information of parental haplotypes.

Testing for the inheritance of a disease susceptibility gene by analysis of haplotype sharing among affected siblings has been well established for the case where all four parental haplotypes have been ascertained. This paper presents a modification of a published method to cover the situation where there is incomplete information concerning parental haplotypes and this new test is applied in a worked example.

Female↗

PubMed1992

A haplotype-based 'haplotype relative risk' approach to detecting allelic associations.

A novel variation of the Haplotype Relative Risk (HRR) of Rubinstein et al. [Hum Immunol 1981;3:384] is proposed, in order to glean increased information about linkage disequilibrium or allelic associations by analyzing haplotype-based data rather than genotypic data. It is shown that statistical tests based on our design give much higher power than those based on the original HRR approach. Several additional nonparametric tests based on the same data are analyzed, and power is computed for each of them. Further, parametric likelihood methods are applied to testing linkage equilibrium, and estimating delta, the coefficient of linkage disequilibrium, from the same data.

Genetic Linkage↗