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Extended Haplotypes (extended + haplotype)
Selected AbstractsNovel haplotypes in 17q21 are associated with progressive supranuclear palsyANNALS OF NEUROLOGY, Issue 2 2004Pau Pastor MD Progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD) are sporadic neurodegenerative diseases presenting as atypical parkinsonian disorders, characterized by the presence of tau-positive neurofibrillary tangles. Recently, an extended haplotype (H1E) of 787.6kb that comprises several genes including MAPT showed increased association with PSP. The objective of this study was to determine the size of the H1E haplotype associated with PSP and CBD in different populations and to identify specific subhaplotypes in the background of H1E haplotype. Nineteen single nucleotide polymorphisms (SNPs) in the 17q21 region were genotyped in two case,control samples. The SNPs that were associated with higher risk for the disease in the homozygous state delimit a region of more that 1Mb. Haplotype analyses in the Spanish sample showed that the most frequent haplotype found among the patients (H1E,), which extends 1.04Mb and contains several genes such as MAPT, CRHR1, IMP5, Saitohin, WTN3, and NSF. A specific subhaplotype (H1E,A) was present in 16% of PSP patients but was not observed in the controls. Furthermore, the H2E,A haplotype, was rarely present in the disease group suggesting that it plays a protective role. The identification of these specific subhaplotypes that modify risk for PSP/CBD supports the hypothesis that a pathogenic allele exists in a subgroup of PSP patients. Ann Neurol 2004;56:249,258 [source] TRAF1 polymorphisms associated with rheumatoid arthritis susceptibility in Asians and in CaucasiansARTHRITIS & RHEUMATISM, Issue 9 2009Tae-Un Han Objective Recent genome-wide association scans and replication studies of European populations have disclosed several single-nucleotide polymorphisms (SNPs) associated with rheumatoid arthritis (RA) susceptibility. The aim of this study was to evaluate the RA-associated loci by genotyping previously reported SNPs and additional tag SNPs in a Korean population. Methods A total of 1,316 unrelated RA patients and 1,006 controls were genotyped for 12 SNPs identified in genome-wide scans and for 12 additional tag SNPs in IL2RB, OLIG3,TNFAIP3, PTPN22, and TRAF1,C5, and the findings were statistically compared. Results None of the SNPs tested was associated with RA susceptibility, except rs7021206 in TRAF1 intron 3 (P = 0.0032) and, among the SNPs previously reported, rs6457617 in HLA (P = 4.6 × 10,35). The association of rs7021206 was positive in patients who were seropositive for rheumatoid factor (P = 0.0051) or for anti,cyclic citrullinated peptide autoantibodies (P = 0.0062). However, Korean patients were negative for the association of rs3761847 in the TRAF1,C5 intergenic region previously reported in Caucasians. Linkage disequilibrium between rs3761847 and rs7021206 was not as high in Koreans (r2 = 0.37) as in Caucasians (r2 = 0.67), which explains the lack of association of rs3761847 in Koreans. Accordingly, RA susceptibility was localized to an extended haplotype marked by rs7021206 rather than rs3761847, and SNPs highly correlated with rs7021206 (r2 , 0.81) extended from rs1953126 in the PHF19,TRAF1 intergenic region to rs2900180 in the TRAF1,C5 intergenic region, spanning 66 kb. Conclusion Our results demonstrate that within and around TRAF1, excluding PHF19 and C5, SNPs highly correlated with rs7021206, but not those correlated with rs3761847, are associated with RA in both Asians and Caucasians and are possibly correlated with causative variations. [source] MICA and MICB microsatellite alleles in HLA extended haplotypesINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2001E. Bolognesi Summary The present study is a contribution to the definition of the linkage disequilibrium relationship of MICA and MICB with adjacent loci and to the characterization of extended HLA haplotypes. These issues are of importance for the identification of disease associations and for a better definition of donor,recipient compatibility in bone-marrow grafts through the typing of haplospecific markers. The distribution of the five alleles of MICA and the 13 alleles of MICB microsatellites, located, respectively, in MICA transmembrane exon 5 and in MICB intron 1, was examined in 133 healthy Italian individuals previously typed for HLA class I, class II and complement loci and for the TNFa microsatellite. The MICB microsatellite was also analysed in 49 HTCLs for which MICA typing was already available. Very strong linkage disequilibria with HLA-B and TNFa were detected in the Italian population for both MICA and MICB microsatellite alleles, in spite of the high mutability rate of the larger MICB alleles. Some strong associations were also detected between MICB and DRB1. The strongest associations (P < 0.001, D, > 0.7) were those of MICA-A4 with HLA-B18, B27 and TNFa1, MICA-A5 with HLA-B35, B61 and B62, MICA-A5.1 with HLA-B7, B8, B13, B63 and MICB-CA24, MICA-A6 with HLA-B51, MICA-A9 with HLA-B39, B57 and TNFa2, MICB-CA14 with HLA-B14, B27 and TNFa1, MICB-CA15 with HLA-B52, TNFa4 and TNFa13, MICB-CA17 with HLA-B7 and TNFa11, MICB-CA18 with HLA-B13 and TNFa7, MICB-CA22 with HLA-B57, and MICB-CA24 with HLA-B8 and TNFa2. From pairwise associations in the random panel and results for the homozygous cell lines it was possible to deduce the MICA and MICB microsatellite alleles present in many of the well-known Caucasoid extended haplotypes. [source] Study of Regions of Extended Homozygosity Provides a Powerful Method to Explore Haplotype Structure of Human PopulationsANNALS OF HUMAN GENETICS, Issue 2 2008D. Curtis Summary Previous investigations have reported linkage disequilibrium occurring between nearby polymorphisms, a block-like structure for such relationships, some instances where surprisingly few haplotypes are found and regions of extended homozygosity which are especially marked around centromeres and which are especially common on the X chromosome. We investigated the distribution and nature of regions of extended homozygosity in a sample of 1411 subjects included in a genome wide association study. Regions of extended homozygosity over 1Mb are common, with an average of 35.9 occurring per subject, and containing on average 73 homozygous markers. They have a markedly non-random distribution. They are relatively common on the X chromosome and are seen at centromeres but are also concentrated at other chromosomal regions where presumably recombination is rare. They seem to be a consequence of some haplotypes being very common in the population and although sometimes this reflects the effect of a very common haplotype we also note that there are examples of two or three common haplotypes, each very different from each other, underlying this effect. Regions of extended homozygosity are commoner than previously appreciated. They result from the presence of extended haplotypes with high population frequency. Such regions concentrate in particular locations. The haplotypes involved are sometimes markedly disparate from each other. These regions offer a valuable opportunity for further investigation, in particular with regard to their ancestral history. [source] Relationship of the extended tau haplotype to tau biochemistry and neuropathology in progressive supranuclear palsyANNALS OF NEUROLOGY, Issue 4 2001Wan-Kyng Liu PhD Two extended haplotypes of the tau gene (H1 and H2) have been described. The frequency of H1 haplotype is increased in progressive supranuclear palsy (PSP). PSP is associated with filamentous tau lesions in neurons and glia, which are reportedly composed exclusively of tau isoforms with four repeats in the microtubule-binding domain (4R tau). To determine the influence of the tau haplotype on tau isoform composition and neuropathology, we studied 25 PSP cases and 6 Alzheimer's disease patients matched for age, sex, and postmortem delay. In the basal ganglia, tau and amyloid burdens were determined to see if there was an effect of concurrent Alzheimer-type pathology, and the ratio of 4R to 3R tau was measured in detergent-insoluble tau fractions. Insoluble tau from PSP was not composed exclusively of 4R tau. All brains had a mixture of 4R and 3R tau, but the ratio was different in Alzheimer's disease and PSP. In Alzheimer's disease there was less 4R than 3R tau, whereas the ratio was reversed in PSP. In PSP cases with concurrent Alzheimer-type pathology, the ratio of 4R to 3R was intermediate between Alzheimer's disease and PSP. The H1 haplotype had no effect on the 4R to 3R ratio or on tau and amyloid burdens. In summary, the H1 haplotype does not have a major influence on the pathological or biochemical phenotype of PSP. [source] | ||||||||||