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At least 109 records · Page 6Linked to original sources
PubMed2006

[Colombian haplotypes of the Gaucher disease-causing N370S mutation may originate from a possible common ancestral haplotype].

INTRODUCTION: Gaucher disease is a pan-ethnic condition characterised by glucosylceramide accumulation in macrophages due to glucocerebrosidase deficiency. Its gene, GBA, has been mapped to 1q21 and mutation N370S is the main cause of the disease in western populations, including Colombia. OBJECTIVE: To asses the degree of association between N370S mutation and the alleles of five microsatellites near the mutation site in the GBA locus in nine Colombian Gaucher patients, from the Cundinamarca-Boyacá region. MATERIALS AND METHODS: DNA from patients bearing the N370S mutation, their closest relatives, and 30 controls was taken to PCR-amplify the markers: D1S305, D1S2624, DIS2777, ITG6.6.2 and 5GC3.2. Allele frequencies were calculated, haplotypes inferred and linkage disequilibrium levels between marker alleles and N370S were also estimated. RESULTS: Eleven N370S chromosomes were obtained. A consensus N370S haplotype consisting of the alleles: 222-314-260-301-172 (base pairs) was identified. Each allele corresponding to markers 5GC3.2, ITG6.6.2, D1S277, D1S2624 and D1S305, respectively. There was statistically significant linkage disequilibrium between the alleles of 222, 314, 260, 301 base pairs and the N370S mutation. CONCLUSION: A conserved fraction of the haplotypes suggests that N370S may be present among patients and stem from a single ancestral chromosome for which the ethnic origin is still unclear.

Colombia↗
PubMed1998

[Allelic polymorphism and analysis of haplotypes of the muscle protein kinase genes and haplotype analysis in residents of northwestern Russia and patients with myotonic dystrophy].

The distribution of alleles with various CTG-repeat numbers was studied and the haplotypes for polymorphic sites HhaI and HinfI of mouse muscle protein kinase (DMPK) were analyzed in inhabitants of northwestern Russia and in patients with myotonic dystrophy (90 and 18 chromosomes, respectively). Twelve normal alleles with the triplet-repeat number from 5 to 24 were identified and the alleles with five (42.5%) and 11-13 (37%) repeats were found to be predominant. The bimodal distribution revealed is similar to those described earlier for other populations, however, the frequencies of individual alleles differed from those in populations of Europe and Central Russia. No significant differences in frequencies of CTG alleles were found in 32 normal chromosomes involved in compounds with the mutant chromosomes (i.e., in patients with myotonic dystrophy) as compared to their frequencies in the population. However, almost all mutant chromosomes (16 of 18) had the same haplotype for intragenic polymorphic sites: HhaI-; HinfI+. This haplotype was also inherent in 91% of all chromosomes with CTG5 and all chromosomes with a CTG number more than 15. Possible evolution of chromosomes with different numbers of triplet repeats mediating their expansion and impairing the function are discussed.

Alleles↗
PubMed1995

Genome scanning for complex disease genes using the transmission/disequilibrium test and haplotype-based haplotype relative risk.

Two tests for allelic association were applied to a simulated complex disease for the Genetic Analysis Workshop 9. The transmission/disequilibrium test [Spielman et al., 1993] and the haplotype-based haplotype relative risk approach [Terwilliger and Ott, 1992] were used to detect disease-associated alleles in a set of 360 computer-simulated markers located on six chromosomes and genotyped in 200 nuclear families. This analysis emulates a genome-based search for linked markers. Computer simulations were also performed to clarify statistical properties of the TDT.

Alleles↗
PubMed2004

Analysis of childhood absence epilepsy using haplotype-based haplotype relative risk and transmission disequilibrium test.

The authors performed haplotype-based haplotype relative risk (HHRR) and transmission disequilibrium test (TDT) analysis of childhood absence epilepsy in 30 trios families, using gene typing technology based on microsatellite polymorphic marker. The five microsatellite DNA markers (D8S554, D8S1753, D8S534, D8S1100, D8S1783) used in the study are on chromosome 8q24. HHRR shows D8S554(4) (chi2 = 5.939, P < 0.05), D8S1100(3) (chi2 = 5.081, P < 0.05), D8S1783(6) (chi2 = 4.308, P < 0.05), TDT shows D8S554(4) (chi2 = 4.455, P < 0.05), D8S1783(6) (chi2 = 4, P < 0.05), some signs of association and disequilibrium between these loci and CAE. A suspected association of childhood absence epilepsy in the Chinese population to chromosome 8q24 has been proposed. In addition, it is hypothesized that the CAE gene might have a genetic heterogeneity in the population from a different race.

Asian People↗
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↗
PubMed1987

Microheterogeneity of HLA-DR4 haplotypes: DNA sequence analysis of LD"KT2" and LD"TAS" haplotypes.

We have isolated and sequenced cDNA clones corresponding to the polymorphic alpha and beta chains encoded by the DR and DQ subregions of two HLA-DR4 haplotypes, LD"KT2" and LD"TAS". These two haplotypes are distinguished on the basis of mixed lymphocyte culture typing. The data indicate that the designation of LD"TAS" as a distinct subtype from Dw13 is very likely due to amino acid differences in the DQ beta chain. In contrast, LD"KT2" differs from TAS and Dw13 by a single amino acid substitution at position 37 of the DR beta 1 chain. The functional and evolutionary significance of these polymorphisms is discussed.

Amino Acid Sequence↗
PubMed1990

Differences in gene copy number carried by different MHC ancestral haplotypes. Quantitation after physical separation of haplotypes by pulsed field gel electrophoresis.

We have examined the hypothesis that MHC ancestral haplotypes have a specific content of genes regulating the extent of autoimmune reactions. Gene copy number was quantitated by objective densitometry after PFGE was used to separate heterozygous AHs of different lengths. Initially we analyzed examples of known gene copy number at the C4 and 21 hydroxylase loci and showed that the approach provides predictable results. We then studied heterozygotes containing one characterized and one uncharacterized AH with particular attention to the gene copy number at the C4, Cyp21, and DRB loci. Each AH studied has a characteristic gene copy number at each locus studied. The same may be true of TNF, but other possibilities must be considered. AHs are markers for extensive chromosomal segments including particular numbers of several functional genes. Since AHs mark susceptibility to autoimmune disease, differences in gene copy number may be implicated.

Blotting, Southern↗
PubMed1995

Haplotype analysis of the delta 2642 and (CAG)n polymorphisms in the Huntington's disease (HD) gene provides an explanation for an apparent 'founder' HD haplotype.

The discovery of the intragenic delta 2642 deletion/insertion polymorphism in the Huntington's disease (HD) gene provides a tool to explore HD evolution, as the deletion is rare in normal chromosomes but overrepresented in HD chromosomes. Thus, delta 2642 deletion alleles were thought to mark normal chromosomes that are particularly prone to becoming HD chromosomes. We have examined this polymorphism in a range of human and non-human primate populations. Our results suggest that the deletion event probably occurred in the human lineage on a chromosome with a CAG allele length at the upper end of the normal size range, as the deletion seemed to be only associated with human chromosomes with 20 or more repeats. These deletion chromosomes are prone to expansion into the HD range because they are at the upper end of the normal range. These data explain the apparent 'founder' HD haplotype defined by the deletion and suggest that chromosomes carrying the deletion are no more mutable than non-deletion chromosomes with similar sized CAG repeats.

Alleles↗
PubMed2003

An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries.

We describe a new method for finding haplotype blocks based on the use of the minimum description length principle. We give a rigorous definition of the quality of a segmentation of a genomic region into blocks, and describe a dynamic programming algorithm for finding the optimal segmentation with respect to this measure. We also describe a method for finding the probability of a block boundary for each pair of adjacent markers: this gives a tool for evaluating the significance of each block boundary. We have applied the method to the published data of Daly et al. The results are in relatively good agreement with the published results, but also show clear differences in the predicted block boundaries and their strengths. We also give results on the block structure in population isolates.

Algorithms↗
PubMed1985

Haplotype-specific suppression of antibody responses in vitro. III. Haplotype-specific suppressor factor (TsF-H) binds to but fails to suppress responses by the I-A mutant strain B6.C-H-2bm12.

Spleen cells from C57BL/6 and B6.C-H-2bm12 mice, both responder strains to GAT, differ in their ability to be suppressed by the monoclonal I-A-restricted, nonantigen-specific, but haplotype-specific suppressor factor, TsF-H, from the hybridoma 266A4.5. Whereas GAT-specific responses by C57BL/6 spleen cells are susceptible to TsF-H-mediated suppression, responses by bm12 spleen cells are nonsuppressible under the same conditions. Responses of both C57BL/6 and bm12 spleen cells are suppressed by monoclonal GAT-specific suppressor factors. The inability of TsF-H to suppress responses by the bm12 spleen cells presumably reflects the effects of the mutation in the beta-chain of the I-A antigen in this strain on the required I-A restriction between TsF-H and target cell for manifestation of suppressive activity. The data are discussed in terms of involvement of I-A or recognition of I-A in mediating suppression.

Absorption↗