SEARCH · PubMed Health

Results for “Haplotype structures”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources

PubMed2003

Genetic analysis of human remains found in two eighteenth century Yakut graves at At-Dabaan.

We extracted DNA from three skeletons belonging to the Yakut population, which were excavated from the At-Dabaan site (dating back 300 years) in the Sakha Republic (Russia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these three skeletons were not close relatives but probably linked to the same clan structure. Comparison of their haplotypes with the haplotypes of 8,774 Eurasian individuals suggested a relative specificity and continuity of part of the Yakut mitochondrial gene pool during the last 3 centuries.

Anthropology, Physical↗

PubMed2006

Distribution of chloroplast DNA haplotypes in the contact zone of Fagus crenata in the southwest of Kanto District, Japan.

We have investigated cpDNA haplotype distribution in 24 populations of Fagus crenata in the southwest of Kanto District, Japan, and clarified the extent of intermixing of haplotypes in the contact zone by additional fine-scale analysis of two areas. Two cpDNA haplotypes belonging to different lineages were detected, and their distribution had geographical structure. Intermixed populations with the two haplotypes were limited to a narrow area. The geographical boundary between the haplotypes extended from Hakone to the west of the Kanto Mountains through the northern foot of Mt Fuji. No relationship was observed between the boundary location and the current topography of the southwest of Kanto District.

DNA, Chloroplast↗

PubMed2004

Both risk alleles for FcgammaRIIA and FcgammaRIIIA are susceptibility factors for SLE: a unifying hypothesis.

The aim of this study was to analyze in families with SLE for the presence of linkage and the structure and transmission of haplotypes containing alleles for the low-affinity Fcgamma receptors. The Fcgamma receptor polymorphisms FcgammaRIIA-131R/H, FcgammaRIIIA-176F/V and FcgammaRIIIB-NA1/2 and a polymorphism in the FcgammaRIIB gene were genotyped with RFLP, allele-specific PCR or pyrosequencing. Individual SNPs and haplotypes were tested for linkage in multicase families and for association using contingency tables, transmission disequilibrium test and affected family-based control groups in Swedish and Mexican single-case families. No linkage or association could be detected using the FcgammaR polymorphisms in the multicase families. However, an association was found for both FcgammaRIIA-131R and IIIA-176F alleles in the single-case families, but not for IIIB or IIB. Allelic association to SLE was found for a haplotype that included both risk alleles, but not in haplotypes where only one or the other was present. We propose that FcgammaRIIA-131R and FcgammaRIIIA-176F are both risk alleles for SLE transmitted primarily, but not exclusively on a single major haplotype that behaves functionally in a situation similar to that of compound heterozygozity.

Alleles↗

PubMed2004

'What's larvae got to do with it?' Disparate patterns of post-glacial population structure in two benthic marine gastropods with identical dispersal potential.

In marine environments, many species have apparently colonized high latitude regions following the last glacial maximum (LGM) yet lack a life-history stage, such as a free-living larva, that is clearly capable of long-distance dispersal. Two hypotheses can explain the modern high latitude distributions of these marine taxa: (1) survival in northern refugia during the LGM or (2) rapid post-glacial dispersal by nonlarval stages. To distinguish these two scenarios, I characterized the genetic structure of two closely related northeastern Pacific gastropods that lack planktonic larvae but which have distributions extending more than 1000 km north of the southern limit of glaciers at the LGM. Despite having identical larval dispersal potential, these closely related species exhibit fundamentally different patterns of genetic structure. In Nucella ostrina, haplotype diversity among northern populations (British Columbia and Alaska) is low, no pattern of isolation by distance exists and a coalescent-based model of population growth indicates that during the LGM population size was reduced to less than 35% of its current size. In the congeneric and often sympatric N. lamellosa, northern populations harbour a diversity of ancient private haplotypes, significant evidence of isolation by distance exists and regional subdivision was found between northern (Alaska) and southern (southern British Columbia, Washington and Oregon) populations. Estimates of coalescent parameters indicate only a modest reduction in population size during the LGM and that northern and southern populations of N. lamellosa split approximately 50 Kyr before the LGM. The patterns are consistent with the hypothesis that N. ostrina recently reinvaded the northeastern Pacific but N. lamellosa survived the LGM in a northern refuge. A comparison of similar studies in this region indicates that depleted levels of genetic variation at high latitudes--evidence suggestive of recent colonization from a southern refuge--is more common among intertidal species that live relatively high on the shore, where exposure times to cold stress in air are longer than for species living lower on the shore. These data suggest that for some faunas, ecological differences between taxa may be more important than larval dispersal potential in determining species' long-term biogeographical responses to climate change.

Animals↗

PubMed2005

Diversity of the CYP21P-like gene in CYP21 deficiency.

More than 90% of cases of congenital adrenal hyperplasia (CAH) are caused by mutations of the CYP21 gene. The occurrence of defective CYP21 genes, including 15 mutations, has been attributed to intergenic recombination of DNA sequences from CYP21P, and shows no influence on the RP1-C4A-CYP21P-XA-RP2-C4BCYP21- TNXB gene locus on chromosome 6p21.3. However, multiple gene deletions in this region produce at least three categories of gene arrangements: (a) C4A-CYP21P/CYP21-TNXB, in which there is a CYP21P/CYP21 fusion gene; (b) C4A-XCYP21-TNXB, where XCYP21 indicates that the CYP21 gene contains mutations of IVS2 (-12A/C>G and 707-714delGAGACTAC); and (c) C4A-CYP21P-TNXA/TNXB, in which the TNX A and B genes are fused. Among them, seven different structures of the CYP21 haplotype were found at these three loci. Formation of the C4A-CYP21P/CYP21-TNXB locus produced four distinct CYP21P/CYP21 chimeras. The C4A-XCYP21-TNXB locus contained the IVS2 mutation -12A/C>G and 707-714delGAGACTAC from the XCYP21 gene; and two kinds of TNXA/TNXB hybrids were found in the C4A-CYP21P-TNXA/TNXB locus. The seven different CYP21 alleles produced 3.2 kb Taq I fragments caused by deletion of the RP2-XA-C4B locus. Therefore, production of a 3.2-kb CYP21 allele shows diversity, but is not a unique feature of the CYP21P gene. Most of these gene arrangements probably exist in the C4A-XCYP21-TNXB and C4A-CYP21P/CYP21-TNXB gene loci. The existence of the C4A-CYP21P-TNXA/TNXB locus might not be common in CAH patients with 21-hydroxylase deficiency.

Adrenal Hyperplasia, Congenital↗

PubMedDate not supplied

Intraspecific genetic variation in Paramecium revealed by mitochondrial cytochrome C oxidase I sequences.

Studies of intraspecific genetic diversity of ciliates, such as population genetics and biogeography, are particularly hampered by the lack of suitable DNA markers. For example, sequences of the non-coding ribosomal internal transcribed spacer (ITS) regions are often too conserved for intraspecific analyses. We have therefore identified primers for the mitochondrial cytochrome c oxidase I (COI) gene and applied them for intraspecific investigations in Paramecium caudatum and Paramecium multimicronucleatum. Furthermore, we obtained sequences of the ITS regions from the same strains and carried out comparative sequence analyses of both data sets. The mitochondrial sequences revealed substantially higher variation in both Paramecium species, with intraspecific divergences up to 7% in P. caudatum and 9.5% in P. multimicronucleatum. Moreover, an initial survey of the population structure discovered different mitochondrial haplotypes of P. caudatum in one pond, thereby demonstrating the potential of this genetic marker for population genetic analyses. Our primers successfully amplified the COI gene of other Paramecium. This is the first report of intraspecific variation in free-living protozoans based on mitochondrial sequence data. Our results show that the high variation in mitochondrial DNA makes it a suitable marker for intraspecific and population genetic studies.

Animals↗

PubMed2004

A novel tetrameric short tandem repeat located in the 3' flanking region of the human ABO-secretor gene (FUT2) and association between FUT2 and FUT2/01 loci.

We found a novel polymorphic short tandem repeat (FUT2/01), 3.8 kb downstream of the coding region of FUT2. Seventeen length and 33 sequence variants were identified in 300 individuals representing three major human populations. Africans (Xhosa) and Europeans were characterized by high microvariation, and Japanese were characterized by a simple repeat structure. All exhibited high haplotype diversity.

ABO Blood-Group System↗

PubMed1984

The OLA major histocompatibility complex of sheep. Study of six new factors and evidence of a third locus of the complex: OLA-C.

6 new factors and 2 specificities 8L (A8-like) and 6L (B6-like) are described in sheep, in addition to the previously described 11 factors. 3 new factors are the products of three alleles (C14, C15, C17) at a third OLA-C locus of the OLA major histocompatibility complex, closely linked to the OLA-A and B loci. 2 other factors are the products of 2 alleles (A13 and B12) at OLA-A and B loci. The last new factor (16) is also the product of an OLA gene, the locus of which is not yet defined. An additional 8L factor is defined as the product of an OLA-A or B new allele. On the whole, 18 factors now known in sheep are the products of genes at 5 loci. 16 factors are distributed in 3 allelic series corresponding to the 3 OLA-A, B and C loci (the last 2 factors depend each on one of the two loci OL-X and OL-Z). 28 haplotypes are described in the studied 'Préalpe' flock. The new factors identify 6 haplotypes which were previously undetermined, and they subdivide some previously described haplotypes; nevertheless, OLA genetic structure appears to have changed little in the flock for 10 years. Genes at the three OLA loci are in linkage disequilibrium.

Alleles↗

PubMed2006

Assaying chromosomal inversions by single-molecule haplotyping.

Inversions are an important form of structural variation, but they are difficult to characterize, as their breakpoints often fall within inverted repeats. We have developed a method called 'haplotype fusion' in which an inversion breakpoint is genotyped by performing fusion PCR on single molecules of human genomic DNA. Fusing single-copy sequences bracketing an inversion breakpoint generates orientation-specific PCR products, exemplified by a genotyping assay for the int22 hemophilia A inversion on Xq28. Furthermore, we demonstrated that inversion events with breakpoints embedded within long (>100 kb) inverted repeats can be genotyped by haplotype-fusion PCR followed by bead-based single-molecule haplotyping on repeat-specific markers bracketing the inversion breakpoint. We illustrate this method by genotyping a Yp paracentric inversion sponsored by >300-kb-long inverted repeats. The generality of our methods to survey for, and genotype chromosomal inversions should help our understanding of the contribution of inversions to genomic variation, inherited diseases and cancer.

Chromosome Inversion↗

PubMed2006

A coalescence-guided hierarchical Bayesian method for haplotype inference.

Haplotype inference from phase-ambiguous multilocus genotype data is an important task for both disease-gene mapping and studies of human evolution. We report a novel haplotype-inference method based on a coalescence-guided hierarchical Bayes model. In this model, a hierarchical structure is imposed on the prior haplotype frequency distributions to capture the similarities among modern-day haplotypes attributable to their common ancestry. As a consequence, the model both allows distinct haplotypes to have different a priori probabilities according to the inferred hierarchical ancestral structure and results in a proper joint posterior distribution for all the parameters of interest. A Markov chain-Monte Carlo scheme is designed to draw from this posterior distribution. By using coalescence-based simulation and empirically generated data sets (Whitehead Institute's inflammatory bowel disease data sets and HapMap data sets), we demonstrate the merits of the new method in comparison with HAPLOTYPER and PHASE, with or without the presence of recombination hotspots and missing genotypes.

Algorithms↗

PubMed1999

The colonization history and present-day population structure of the european great tit (Parus major major)

The colonization history and present-day population structure of the European subspecies of the great tit Parus major major were studied using mitochondrial control region sequences. One major haplotype was found in all but one of the eight sampled populations from Spain to northern Finland. The other haplotypes differed from the common one by just a few substitutions; the overall nucleotide diversity was 0.00187 and haplotype diversity 0.8633. No population structuring was detected. The mismatch distribution followed the expected distribution of an expanding population. The estimated time to the most recent common ancestor coincides with the last glacial period. The results suggest that P. m. major survived the last glacial period in a single isolated refuge probably by the Mediterranean Sea. This was followed by rapid colonization of the European continent and population growth. The most recent range expansion northwards is still occurring. Gene flow between the sampled populations is extensive. It is aided by juvenile dispersal, long-distance movements of juvenile flocks and partial migration in the northern parts of the great tit's range.

Journal Article↗

PubMed2001

An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations.

The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were.86-.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, phi(ST) statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure.

Africa↗

PubMed1986

Nonhomologous pairing in mice heterozygous for a t haplotype can produce recombinant chromosomes with duplications and deletions.

We have investigated the structure and properties of a chromosomal product recovered from a rare recombination event between a t haplotype and a wild-type form of mouse chromosome 17. Our embryological and molecular studies indicate that this chromosome (twLub2) is characterized by both a deletion and duplication of adjacent genetic material. The deletion appears to be responsible for a dominant lethal maternal effect and a recessive embryonic lethality. The duplication provides an explanation for the twLub2 suppression of the dominant T locus phenotype. A reanalysis of previously described results with another chromosome 17 variant called TtOrl indicates a structure for this chromosome that is reciprocal to that observed for twLub2. We have postulated the existence of an inversion over the proximal portion of all complete t haplotypes in order to explain the generation of the partial t haplotypes twLub2 and TtOrl. This proximal inversion and the previously described distal inversion are sufficient to account for all of the recombination properties that are characteristic of complete t haplotypes. The structures determined for twLub2 and TtOrl indicate that rare recombination can occur between nonequivalent genomic sequences within the inverted proximal t region when wild-type and t chromosomes are paired in a linear, nonhomologous configuration.

Alleles↗

PubMed2006

Diverse structures of chimeric CYP-REP7/6-containing CYP2D6 and a novel defective CYP2D6 haplotype harboring single-type *36 and CYP-REP7/6 in Japanese.

Chimeric REP7/6 has been used as a marker of CYP2D6 deletion, such as for CYP2D6*5. However, the CYP2D6*10D (*10D) haplotype found in a Japanese population consist of CYP2D6*10B, CYP2D7P-derived 3'-flanking region, and a chimeric repetitive sequence, CYP-REP7/6 (REP7/6) (Ishiguro et al. Clin. Chim. Acta. 2004: 347, 217-221). From our analysis, REP7/6 was found in 26 out of 254 Japanese subjects. Thus, the REP7/6-containing CYP2D6 genes (2D6-REP7/6) were analyzed in detail. In order to specifically detect the 2D6-REP7/6 structure, primers were designed in CYP2D6 intron 6 and the REP7/6 3'-flanking region. Among 26 subjects analyzed by PCR, 5 had 2D6-REP7/6. The other 21 subjects were confirmed to have *5 by another *5-specific primer set. Three out of five subjects with 2D6-REP7/6 had the *10D structure. However, further analysis by PCR and sequencing revealed that their haplotypes were further divided into tandem-type *36-*10D (n=2) and single-type *10D (n=1). The remaining two subjects had a novel type of a *36-containing defective structure that consists of CYP2D6*36 and 3'-flanking REP7/6 (single-type *36-REP7/6). Then, REP7/6 sequences in *5, *10D, *36-*10D, and single-type *36 were determined and classified into 5 types: types A to D for *5, type E for *10D and *36-*10D, and type F for *36. These findings could be useful for accurate determination of *5 and REP7/6-harboring aberrant CYP2D6 haplotypes.

Asian People↗

PubMed2006

Genetic diversity of Chinese water deer (Hydropotes inermis inermis): implications for conservation.

The Chinese water deer (Hydropotes inermis inermis) is endemic to China. Historically, the species was widely distributed, but now, habitat loss and poaching have reduced its range and number drastically. In order to provide useful information for its conservation, we have investigated the genetic diversity and population structure of the Chinese water deer by analyzing the 403 bp fragment of the mitochondrial DNA (mtDNA) control region (D-loop). Eighteen different haplotypes were detected in 40 samples. Overall, Chinese water deer have a relatively high-genetic diversity compared to other rare cervid species, with a haplotype diversity of 0.923+/-0.025 and nucleotide diversity of 1.318 +/- 0.146%. No obvious phylogenetic structure among haplotypes was found for samples of different origin. An analysis of molecular variance (AMOVA) showed significant differentiation between the Zhoushan and the mainland population (F(ST)= 0.088, P < 0.001; Phi( ST ) = 0.075, P = 0.043), which suggests that exchanges of individuals between Zhoushan and the mainland should be avoided. We also recommend that a breeding center be set up for the mainland population.

Animals↗

PubMed1995

The same esterase B1 haplotype is amplified in insecticide-resistant mosquitoes of the Culex pipiens complex from the Americas and China.

In Culex pipiens, overproduction of nonspecific esterases is a common mechanism of resistance to organophosphate insecticides. The esterases are attributed to closely linked loci named A and B, and overproduction of all esterases B is due to gene amplification. In order to determine if the esterase B1 identified by electrophoretic studies in Culex pipiens mosquitoes from different countries is overproduced due to the amplification of the same DNA haplotype, the amplified region encompassing the structural esterase B1 gene was characterized by restriction mapping and RFLP. The same amplified haplotype was found in mosquitoes with an esterase B1 protein, independently of their geographical origin: French Guiana, Venezuela, Puerto Rico, California and China. Large variations in amplification levels were observed. It is concluded that B1 amplification has a unique origin, either in America or in Asia, and has subsequently spread by migration. This migration is more limited than that of A2-B2 esterases, since B1 is confined to the Americas, the Caribbean and part of China, whereas the A2-B2 distribution now includes the Americas, the Caribbean, Asia, Africa, the Pacific Islands and Europe.

Americas↗

PubMed1990

Haplotype analysis of the human apolipoprotein B mutation associated with familial defective apolipoprotein B100.

Haplotype analysis was conducted on the mutant allele of 14 unrelated subjects heterozygous for a mutation in the codon for amino acid 3500 of human apolipoprotein B100. This mutation is associated with defective binding of low-density lipoprotein to the low-density lipoprotein receptor and with moderate hypercholesterolemia. Ten markers were used for haplotyping: eight diallelic markers within the structural gene and two hypervariable loci flanking the gene. Seven of eight unequivocally deduced haplotypes were identical, and one revealed only a minor difference at one of the hypervariable loci. The genotypes of the six other affected subjects were consistent with this same assigned haplotype. These data are consistent with a common ancestral chromosome and provide no evidence for a recurrent mutation at this potentially hypermutable CG dinucleotide, despite the fact that this mutation is not rare.

Alleles↗

PubMed1986

Sequence analysis and structure-function correlations of murine q, k, u, s, and f haplotype I-A beta cDNA clones.

I-A beta-chain cDNA clones from mice of the q, k, u, s, and f haplotypes have been isolated and sequenced. Nucleotide sequence comparisons among these five A beta chains show considerable allelic variation in the region encoding the first external (beta 1) domain of the mature A beta protein. The beta 1 domain variability is clustered into three discrete regions, two of which divide the A beta chains into subgroups, suggesting an evolutionary history for the separation of alleles in inbred strains of mice. The amino acid sequences of these five chains are compared to each other and to previously published I-A beta chains. Correlations are made between the primary structural differences and the serologic and immune response characteristics mapping to the I-A subregion.

Amino Acid Sequence↗