SNPs with tight Cr4-linkage were further converted to TaqMan assays to confirm their effectiveness as MAS tools. (frontiersin.org)
Findings from these studies have been confirmed in meta-analyses wherein the associated SNPs are in strong linkage disequilibrium (LD) with one another. (biomedcentral.com)
The significant candidates show an enrichment for nucleotide polymorphisms (SNPs) over gene presence-absence variation (PAV), and for five traits, candidates are enriched in large linkage groups, a possible signature of epistasis. (psu.edu)
RESULTS: The study detected association of several TNF SNPs and established linkage of the locus to juvenile oligoarthritis. (ox.ac.uk)
Northwestern University/Feinberg School of Medicine, Chicago, Il- versity and strong linkage disequilibrium. (cdc.gov)
Locus3
The detection of causal genes for diseases impacted by locus heterogeneity is difficult with genetic analysis methods such as linkage analysis and genome sequencing. (wikipedia.org)
We apply eCAVIAR to the Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) dataset and GTEx dataset to detect the target gene and most relevant tissue for each GWAS risk locus. (zarlab.xyz)
For a third locus, detectable by the classical transmission-disequilibrium test, a substantial increase of power of detection is shown. (biomedcentral.com)
Loci8
Integration of GWAS and eQTL data is challenging due to the uncertainty induced by linkage disequilibrium (LD), the non-random association of alleles at different loci, and presence of loci that harbor multiple causal variants (allelic heterogeneity). (zarlab.xyz)
Further, eCAVIAR detects a large number of loci where the GWAS causal variants are clearly distinct from the causal variants in the eQTL data. (zarlab.xyz)
With an appropriate choice of covariate, both approaches allow detection of two loci that are undetectable by the classical transmission-disequilibrium test. (biomedcentral.com)
D′ can therefore take on values between 0 and 1, and it is a measure of linkage disequilibrium that is normalized for variations in allele frequencies at the two loci. (musculoskeletalkey.com)
Application of quantitative genetics methodology in fact supports the presence of 4 as yet unidentified AD-associated loci in the human genome, each expected to affect age of onset (AoO) as much or more than APOE [ 6 ]. (biomedcentral.com)
Existing hybrid inference methods assume that alleles at different loci undergo independent assortment (are unlinked or in population linkage equilibrium). (nfshost.com)
B. burgdorferi is transmitted to humans disequilibrium among genetic loci can result from several during the blood meal of an infected Ixodes tick, predomi- evolutionary and ecologic forces in addition to small popu- nantly Ixodes scapularis in North America ( 2 ). (cdc.gov)
Genes5
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)
Single SNP association study is a popular method to detect genes that are susceptible to human diseases. (biomedcentral.com)
To detect these cues, moths have evolved families of genes encoding elements of the peripheral olfactory reception system, including odor carriers, receptors and degrading enzymes. (inra.fr)
Out of these, eight genes of 336 oak individuals growing in Austria have been detected with a total number of 158 polymorphic sites. (biomedcentral.com)
We have characterized 183 alleles of drought related genes from oak species and detected first evidences of natural selection. (biomedcentral.com)
Genetic6
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)
Although bacteria should be amenable to GWAS, few GWAS have been conducted on bacteria, and the extent to which nonindependence among genomic variants (e.g., linkage disequilibrium [LD]) and the genetic architecture of phenotypic traits will affect GWAS performance is unclear. (psu.edu)
Signatures of genetic bottlenecks were detected in all 8 populations after 2003 using the M -ratio method, but in no populations when using a heterozygosity excess method, indicating differential sensitivity of bottleneck detection methods. (biomedcentral.com)
Exploring the Performance of Multifactor Dimensionality Reduction in Large Scale SNP Studies and in the Presence of Genetic Heterogeneity among Epistatic Disease Models. (psu.edu)
Comparison of approaches for machine learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology. (psu.edu)
These studies were commonly performed using a small number of genetic markers [ 4 ], and consequently were underpowered to detect true effects. (biomedcentral.com)
Genomic6
We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and non-dune populations. (borealisdata.ca)
For 11 traits, we find genotype-phenotype associations that are stronger than expected by chance, with the candidates in relatively small linkage groups, indicating that LD does not preclude resolving association candidates to relatively small genomic regions. (psu.edu)
To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 718,256 oligonucleotide probes with a median probe spacing of 500 bp. (biomedcentral.com)
We detected CNVs in rice by array-based comparative genomic hybridization. (biomedcentral.com)
CNVs can be detected using cytogenetic techniques such as fluorescent in situ hybridization, array-based comparative genomic hybridization, and SNP genotyping arrays. (biomedcentral.com)
Genomic datasets include thousands of markers that are located on the same chromosome and are in populationlinkage disequilibrium which violate this assumption. (nfshost.com)
Genome2
Here, we assess the presence of candidate signatures of positive selection in their genome, with the aim to provide qualitative insights about the corresponding selective pressures. (nature.com)
Background: Recently, we have obtained evidence for linkage between Der p 1-specific IgE antibodies and markers on chromosome 6p21 (HLA-D region) in a genome-wide screening in Caucasian families recruited as a part of the Collaborative Study on the Genetics of Asthma (CSGA). (tmu.edu.tw)
Heterogeneity1
Consequently, many statistical methods have been developed that allow for the detection of linkage and/or association signals in the presence of heterogeneity. (biomedcentral.com)
Populations2
The Andean altiplano has long been a focus of research into high-altitude adaptation for a number of reasons including relative accessibility, the large numbers of altitude-adapted species that thrive there, the presence of large indigenous human populations and the early involvement in the field by such eminent Latin American biologists as Carlos Monge M., his son Carlos Monge C. and Alberto Hurtado. (silverchair.com)
linkage disequilibrium within B. burgdorferi populations likely result from small effective population sizes ( 9-11 ). (cdc.gov)
Alleles2
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)
In the case of systemic lupus erythematosus (SLE) and related illnesses, many of the HLA class II alleles are associated with the presence of specific autoantibodies or clinical phenotypes. (musculoskeletalkey.com)
Gene-gene interactions1
The reversal of risk embodied in this interaction powerfully supports the importance of considering the role gene-gene interactions play in the etiology of complex biological diseases and demonstrates the importance of using multiple analytic methods to detect well-supported gene-gene interactions. (biomedcentral.com)
Association3
Herein, we introduce two slightly different approaches, inspired by OSA and by Spielman's transmission-disequilibrium test (TDT) [ 4 ], for family-based linkage and association testing. (biomedcentral.com)
The OSA-TDT approach is very similar to Hauser's approach, and aims at detecting linkage and association of a marker with the disease in a covariate-ordered subset of families. (biomedcentral.com)
The chi-square and extended transmission disequilibrium tests were used to test for association and linkage, respectively. (ox.ac.uk)
Recombination1
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)
Phenotypic1
Phenotypic segregation for presence/absence of stem symptoms was observed in four seed families. (frontiersin.org)
Markers2
TDT was conducted between the presence of specific IgE antibodies toward each of 12 different Der p polypeptides and 4 polymorphic markers on chromosome 6p21. (tmu.edu.tw)
Deciding who is really inbred is a methodological challenge where multi-point approaches can be very helpful once the set of SNP markers is filtered to remove linkage disequilibrium. (biomedcentral.com)
Significant1
The aim of OSA is to test whether significant linkage can be observed in a subset consisting of the first families of this ordering, up to a certain rank that is not predefined. (biomedcentral.com)
Genotypes1
To study cellular immune reactivity to CII in patients with RA and in healthy control individuals and to correlate this reactivity to HLA class II genotypes and to the presence of antibodies to CII in serum. (biomedcentral.com)
Transmission-dise1
Objective: Specific IgE antibodies toward different Dermatophagoides pteronyssinus (Der p) polypeptides were detected by immunoblotting analysis, and the transmission/disequilibrium test (TDT) was performed between specific IgE responsiveness toward each different Der p polypeptide and markers on chromosome 6p21 to better clarify the genetic contribution of HLA-D genes. (tmu.edu.tw)
Frequency1
With few exceptions, generally comparable measures of viral diversity and mutational frequency were detected following homologous virus infection of both respiratory-origin and ocular-origin tissue constructs. (cdc.gov)
Methods2
This is what led the researchers to use methods such as ChromoPainter/ fineStructure/ Globetrotter that can squeeze out fine-scale population structure by exploiting linkage disequilibrium. (blogspot.com)
In this study 465 clinical samples were tested using PCR and the results obtained indicates that this approach offers may advantages over conventional methods and could be used to detect Mycobacterium tuberculosis in clinical samples. (who.int)
Absence1
In addition, a trend was observed between the presence or absence of the +1073 C allele and the level of astrocytic activation in the brain of AD cases. (bmj.com)
Traits1
For other traits, apparently strong associations were not stronger than the range of associations detected in permuted data. (psu.edu)
Analysis2
The ordered subset analysis (OSA) [ 1 ] was designed to perform linkage analysis based on the ordering of families on the values of a covariate (e.g., the average AAO of the affected members of a family). (biomedcentral.com)
Analysis of the hemp leaf extract and functional groups that were associated with ZnONP-HL and CuONP-HL confirmed the presence of terpenes, flavonoids, and phenolic compounds. (cdc.gov)
Single1
However, the degree of linkage disequilibrium across the entire intron 1 of FTO has prevented a single potentially functional SNP from being identified, although trans-ethnic comparison has permitted a degree of fine mapping of the region [ 11 ]. (biomedcentral.com)
Data1
Edwards T.L., Bush W.S., Turner S.D., Dudek S.M., Torstenson E.S., Schmidt M., Martin E., Ritchie M.D. 2008 Generating linkage disequilibrium patterns in data simulations using genomeSIMLA. (psu.edu)
Clinical1
The objective of the study was to develop a rapid method to detect Mycobacterium tuberculosis from clinical samples and the applicability of DNA amplification techniques to a developing country like Sri Lanka. (who.int)
Disease1
The evidence for an autoimmune etiology includes pathological findings of infiltrating T cells, the presence of antigen-antibody complexes in affected cartilage, cellular and humoral responses against collagen type II and other collagen antigens, and the observation that immunosuppressive regimens most often suppress the disease. (medscape.com)
Symptoms1
A laboratory evaluation commensurate with the spectrum of reported symptoms is indicated to ascertain the presence of complicating conditions. (medscape.com)