Linkage disequilibrium and recombination analyses. Medical search. Frequent questions

Analysis of linkage disequilibrium in Scottish families showed significant non-random association between the HD gene and alleles at the D4S95 and D4S98 loci. (bmj.com)
A genome-wide map of single nucleotide polymorphisms (SNP) and a pattern of linkage disequilibrium (LD) between their alleles are being established in three main ethnic groups. (ox.ac.uk)
Existing hybrid inference methods assume that alleles at different loci undergo independent assortment (are unlinked or in population linkage equilibrium). (nfshost.com)
Lack of linkage disequilibrium (nonrandom association of alleles over loci) indicates that horizontal transfer and recombination of metabolic enzyme genes have contributed to the generation of chromosomal diversity in H. pylori. (houstonmethodist.org)
It will also be fascinating to study more finely the degree and extent of genomic differentiation at these two loci and to assess whether recombination suppression has extended stepwise away from the sex and self-incompatibility loci, as can be expected under some hypotheses, such as the sheltering of deleterious alleles near permanently heterozygous alleles [7]. (peercommunityin.org)
The intense selection pressures during inbreeding favor the coinheritance of optimal sets of alleles among these genetically linked, functionally related genes, resulting in extensive domains of linkage disequilibrium (LD) among a set of 60 genetically diverse inbred strains. (jax.org)
Recombination that disrupts the preferred combinations of alleles reduces the ability of offspring to survive further inbreeding. (jax.org)
Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. (borealisdata.ca)
Recent studies have shown that susceptibility to either CVID or IgAD may be linked to specific alleles of the major histocompatibility complex, suggesting that these alleles, or alleles of closely linked genes with which they are in linkage disequilibrium, are somehow involved in the pathogenesis of CVID and IgAD. (medscape.com)

These regions also show high linkage disequilibrium and high heterozygosity between, but not within arrangements, consistent with the behavior of large inversions, an inference subsequently validated in part by comparative genetic mapping. (borealisdata.ca)
These results were consistent in analyses that excluded SNPs in high linkage disequilibrium. (biomedcentral.com)

In a Scottish family in which Huntington's disease (HD) was segregating, recombination was observed between the D4S115/S111 and D4S43/S95 loci, with the HD gene associated with the more proximal D4S43/S95 locus. (bmj.com)
Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)
Classical linkage mapping based on biparental populations was used to dissect Quantitative Trait Loci (QTL) for SHR resistance. (biomedcentral.com)
4] confirmed that the sex and self-incompatibility loci are located in two distinct linkage groups and correspond to XY-like systems. (peercommunityin.org)
In order to increase the number of loci discovered (and their explanatory power), substantial efforts have been made to obtain larger sample size by genotyping large cohorts [ 5 , 6 ] and by relying on meta-analysis. (biorxiv.org)
This is reflected respectively by i) variation in polymorphism within and between populations and ii) linkage disequilibrium (LD) between loci. (methodspopgen.com)
The performance of current and newly proposed CODIS core loci sets were evaluated with simplified analyses for adventitious hit rates in reasonably large datasets under single-source profile comparisons, mixture comparisons and kinship searches, and for international data sharing. (biomedcentral.com)
Combining five or six Y-chromosome STR loci with existing autosomal STR loci can produce better performance than the same number of autosomal loci for kinship analysis and still yield a sufficiently low match probability for single-source profile comparisons. (biomedcentral.com)

These results highlight the necessity of a thorough analysis of all reported variants of a candidate gene in the elucidation of genetic susceptibility to a complex disease like hypertension, even when the variants are in the same haplotype block. (tmu.edu.tw)
The multibreed approach increases the number of potentially informative recombination events and reduces the size of the critical haplotype by taking advantage of shortened linkage disequilibrium distances found across breeds. (upenn.edu)
RESULTS: The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBPII, and (ii) PvDBPII appears to contain neutrally evolving codons as well as codons evolving under natural selection. (ox.ac.uk)
5%). Subsequent mutations and recombinations in the ancestral haplotype at which the disease mutation occurred shortened the haplotypes that descended from this ancestor. (biomedcentral.com)
The size of the reduced ancestral haplotype fragments varies as a result of the uneven nature of such recombination and mutation processes. (biomedcentral.com)

Although some single polymorphism analyses of the angiotensinogen (AGT) gene have been found to be associated with hypertension, the results are still inconsistent. (tmu.edu.tw)
A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds. (animbiosci.org)
Based on linkage disequilibrium (LD)-based association mapping used to detect single nucleotide polymorphism (SNP) markers associated with MGR against C. ribicola , MGR in these seed families appears to be controlled by Cr4 or other R genes in very close proximity to Cr4 . (frontiersin.org)

LocusZoom''' is designed to facilitate viewing of local association results together with useful information about a locus, such as the location and orientation of the genes it includes, linkage disequilibrium coefficients and local estimates of recombination rates. (umich.edu)
Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. (cdc.gov)
The presence of linkage disequilibrium between markers in genome-wide association studies (GWAS) often leads researchers to consider the signal associated to multiple neighboring SNPs as indicating the existence of a single genomic locus with possible influence on the phenotype. (biorxiv.org)
The typical association study of candidate regions uses single locus tests, such as the chi-square test or the transmission disequilibrium test [ 4 ]. (biomedcentral.com)

Over time, OspC genes were transferred between strains through recombinations involving the whole or parts of the gene and one or both flanks. (cdc.gov)
Recent human transcriptomic analyses revealed a very large number of testis-enriched genes, many of which are involved in spermatogenesis. (biomedcentral.com)
The recent development of new high-throughput technologies for SNP genotyping has opened the possibility of taking a genome-wide linkage approach to the search for new candidate genes involved in heredity diseases. (biomedcentral.com)
We identified six regions on chromosomes 2, 3, 4, 7, 11 and 14 as candidates to contain genes involved in breast cancer susceptibility, and additional fine mapping genotyping using microsatellite markers around linkage peaks confirmed five of them, excluding the region on chromosome 3. (biomedcentral.com)

Genomic datasets include thousands of markers that are located on the same chromosome and are in population linkage disequilibrium which violate this assumption. (nfshost.com)
The highly skewed distribution of recombination events towards the chromosome ends in zebra finches and other estrildid species may function to minimize crossovers in the inverted regions. (biomedcentral.com)
Problem 2 provided a data set of 2300 single-nucleotide polymorphisms (SNPs) in a 10-Mb region of chromosome 18q, which had shown linkage evidence for rheumatoid arthritis. (biomedcentral.com)

Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene. (ox.ac.uk)
Comparative analysis reveals that the LD patterns are identical in all four European populations tested with two small regions of 1.3 and 5.7 kb at which LD is disrupted completely resulting in three block-like regions over which there is significant and extensive LD. (ox.ac.uk)
Looking for changes in putative adaptations in vertically migrant populations, determining the heritability of putative adaptive traits and genetic association analyses have all been used to evaluate the relative contributions of nurture and nature to the Andean phenotype. (silverchair.com)
Linkage disequilibrium was present in all populations (IAS 0.14 - 0.61) but was higher in those with fewer polyclonal infections, suggesting inbreeding and a clonal population structure. (lshtm.ac.uk)
CONCLUSION: The P. vivax populations circulating in the Peruvian Amazon basin are genetically diverse, strongly differentiated and they have a low effective recombination rate. (lshtm.ac.uk)

In a sample of 461 hypertensive and 327 normotensive patients in Taiwan, we found that -217AA and -6GG homozygotes conferred independently an increased risk to hypertension (P = 0.008 and P = 0.037, respectively), as illustrated by their significant associations with hypertension in both single SNP and pair-wise SNPs analyses. (tmu.edu.tw)
SNPs with tight Cr4-linkage were further converted to TaqMan assays to confirm their effectiveness as MAS tools. (frontiersin.org)
The analysis program pruned away SNPs based on minor allele frequency and strains based on sister-strain similarity. (jax.org)
In order to evaluate the power improvement provided by using SNP markers in a real situation, we have performed a whole genome screen of 19 non-BRCA1/2 breast cancer families using 4720 genomewide SNPs with Illumina technology (Illumina's Linkage III Panel), with an average distance of 615 Kb/SNP. (biomedcentral.com)
Our results show the power increase that SNPs can supply in linkage studies. (biomedcentral.com)
Therefore, we have conducted a linkage study with 4.720 SNPs across the genome in nineteen BRCAX families to identify candidate regions containing BRCAX gene(s). (biomedcentral.com)

This LD pattern suggests combined action of recombination hotspots and founder effects, but cannot be explained by random recombination and genetic drift alone. (ox.ac.uk)

Furthermore, intensive gene flow was discovered among the seven Shandong indigenous breeds, particularly Wulian, Licha, and Heigai, as indicated by the large cluster formed in the principal component analysis scatterplot and small population differentiation (average of 0.1253) among them. (animbiosci.org)
Both linkage disequilibrium and the genetic differentiation (theta) were estimated. (lshtm.ac.uk)
Strong population differentiation (theta = 0.45) was found and the Bayesian inference cluster analysis identified six clusters based on distinctive allele frequencies. (lshtm.ac.uk)

Specifically, PrioriTree provides a suite of functions to generate input files for-and summarize output from-BEAST analyses for performing robust Bayesian inference, data-cloning analyses and assessing the relative and absolute fit of candidate discrete-geographic (prior) models to empirical datasets. (nfshost.com)
Here, we develop a new program Mongrail that implements a full-likelihood Bayesian hybrid inference method that explicitly models linkage and recombination, generating the posterior probability of different F1 or F2 hybrid, or backcross, genealogical classes. (nfshost.com)

A genome-wide germplasm characterization using molecular markers can sympathetic A third limitation is that the results of the meta-analysis in some studies may be influenced alongside cross-cultural issues. (upb.ro)
Under these conditions, recombinations sgobble upween Discount Cialis Soft Tabs markers are common, and linkage disequilibrium wagerween distant markers is weak. (upb.ro)
Genomewide linkage scans have traditionally been performed using low-density maps of microsatellite markers with a spacing of about 10 cM across the genome [ 1 ]. (biomedcentral.com)

used genotyping-by-sequencing to build a genome linkage map of P. angustifolia [4]. (peercommunityin.org)
Checking for population structure is an essential step when performing analyses on genome-level datasets. (methodspopgen.com)
Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. (borealisdata.ca)
Alternatively, significant linkage may have been missed as a result of sub-optimal coverage of the genome by the STR marker set used, which may not have extracted all the inheritance information contained in the dataset. (biomedcentral.com)

CONCLUSION: Our analysis led to the detection of genomic variations between O. sativa cv. (bvsalud.org)
A field of science that combines biology, computer science and statistics to analyse and interpret biological data, particularly genomic and molecular data. (frontlinegenomics.com)

Therefore, association analysis based on haplotypes is believed to be more powerful, in particular if the common disease-common variant theory applies. (biomedcentral.com)

Regardless of whether there was a single major expansion or two, several DNA studies clearly showed that genetic diversity tends to decrease [ 21 , 22 ] and linkage disequilibrium to increase [ 23 , 24 ] at increasing distances from Africa. (biorxiv.org)

You can upload summary results of your own genomewide scan or genomewide meta-analysis and request plots of regions of interest using a web-based form. (umich.edu)
You can upload summary results for your genomewide scan or genomewide meta-analysis and request several plots in one go by uploading a batch file. (umich.edu)
This is handy if you need to generate large numbers of plots or if you want to plot the same set of regions after updating a genomewide analysis (for example). (umich.edu)
Genomewide linkage scans have become a widely used tool in the effort to unravel the genetic bases of human hereditary diseases. (biomedcentral.com)

The features of modern dog breeds that increase the ease of mapping common diseases, such as reduced heterogeneity and extensive linkage disequilibrium, may also increase the difficulty associated with fine mapping and identifying causative mutations. (upenn.edu)

In order to identify breeds that likely share a trait inherited from the same ancestral source, we have used cluster analysis to divide 132 breeds of dog into five primary breed groups. (upenn.edu)

This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage. (upenn.edu)
Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
I study these processes in the field, in the greenhouse, and through comparative (meta-)analyses. (lu.se)

A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. (ox.ac.uk)
This method incorporates the effects of recombination occurring in many past generations into a single analysis and thus, it is complementary to the classical biparental approach [ 27 ]. (biomedcentral.com)

Also linkage disequilibrium analysis reveals differences between clinical and environmental isolates showing a key role of PLB1 allele combinations in host infection as well as the key role of LAC1 allele combinations for survival of the fungus in the environment. (uludag.edu.tr)
In addition, initial sequence analysis reveals highly ordered chromosomal landscapes associated with paralogous gene clusters and distinct functional compartments. (biomedcentral.com)

The AM approach is based on the extent of Linkage Disequilibrium (LD) observed in a set of accessions that are not closely related. (biomedcentral.com)

Phylogenetic and population genetic analyses were performed. (uludag.edu.tr)
Population genetic analysis confirmed that VNI group of isolates were characterized by low variability and clonal expansion while VNIV by a higher variability and a number of recombination events. (uludag.edu.tr)
This study quantified environmental burden of disease by using population health indicators and exploratory factor analysis at the county level across the United States. (cdc.gov)

Diversification requires processes that generate diversity (mutation, recombination) and processes that filter this diversity (drift, natural selection). (lu.se)

A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. (bvsalud.org)

The analysis was integrated with a structural model of PvDBPII, and T- and B-cell epitopes were localized on the 3-D structure. (ox.ac.uk)
Structural analyses of DAD2N242I and DAD2D166A revealed only small differences compared with the structure of the wild-type receptor. (inra.fr)

that lack male recombination [ 10 ]. (biomedcentral.com)

In birds, a detailed analysis is missing although intraspecific inversion polymorphisms are regarded as common. (biomedcentral.com)

Linkage and genetic association studies can be immediately followed by investigation of candidate regions. (biomedcentral.com)
We analyzed data sets of Problems 2 and 3 of Genetic Analysis Workshop 15 and compared HSS and CROSS to conventional association methods. (biomedcentral.com)

Following Dienekes's suggestion on using Pathan and Lithuanian samples as references for ROLLOFF analysis, i decided to undertake a second attempt of formal analysis of admixture and dating of admixture events in Belorusian samples which are available to me: the reference dataset of Belorusians from Behar et al.2011 . (blogspot.com)

Methods We have developed a continuous trait based on disc space narrowing and osteophytes growth which is measurable on all forms of imaging (plain radiograph, CT scan and MRI) and performed a meta-analysis of five cohorts of Northern European extraction each having GWA data imputed to HapMap V.2. (bmj.com)
The results were compared with those obtained previously using a 10 cM microsatellite scan (STR-GWS) and we found lower or not significant linkage signals with STR-GWS data compared to SNP data in all cases. (biomedcentral.com)

One way to address this problem is by combining data from multiple breeds segregating the same trait after initial linkage has been determined. (upenn.edu)

Requires a recombination map. (methodspopgen.com)

Chromatin Immunoprecipitation (ChIP)-Sequencing is a method use to analyse protein interactions with DNA. (frontlinegenomics.com)

Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. (upenn.edu)
Sequence analysis identified 74 sequence types among C. neoformans var. (uludag.edu.tr)

The power of joint- and meta- analyses allowed precise mapping and candidate gene identification, providing the basis for positional cloning of the two major QTLs qHBV4.1 and qHBV11.1. (bvsalud.org)

Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. (ox.ac.uk)

On 1 November 2012 Po-Ru Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K Pickrell, David Reich, Bonnie Berger announced and published their new paper , in which they introduced a new approach that harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. (blogspot.com)

This study is the first GWA meta-analysis of LDD. (bmj.com)

In this analysis, aiming to prepare for marker-assisted selection of drought tolerance in autumn sown faba bean (Vicia faba L.), 196 winter-type and four spring-type inbred lines were genotyped. (uni-goettingen.de)

Anatomy34

Organisms12

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Chemicals and Drugs41

Analytical, Diagnostic and Therapeutic Techniques and Equipment38

Psychiatry and Psychology3

Phenomena and Processes127

Disciplines and Occupations7

Anthropology, Education, Sociology and Social Phenomena5

Technology, Industry, Agriculture2

Humanities1

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