• We estimated the proportion of variance for human height explained by 294,831 SNPs genotyped on 3,925 unrelated individuals using a linear model analysis, and validated the estimation method with simulations based on the observed genotype data. (nih.gov)
  • The most informative subset of SNPs to genotype differs between the two populations. (biomedcentral.com)
  • We provide evidence that the remaining heritability is due to incomplete linkage disequilibrium between causal variants and genotyped SNPs, exacerbated by causal variants having lower minor allele frequency than the SNPs explored to date. (nih.gov)
  • As Vice President of Genome Biology at Perlegen Sciences Frazer worked with David Cox and others to generate the content for the HapMap Phase II project and determined that common structural variants are largely in linkage disequilibrium with common SNPs. (wikipedia.org)
  • is in place for calling SNP variants from the resulting GBS sequences. (frontiersin.org)
  • In the present hypothesis-free study (MR-PheWAS), researchers tested the causal effects of insomnia symptoms on many phenotypes using genetic variants, in this case, single-nucleotide polymorphisms (SNPs) robustly associated with self-reported insomnia symptoms. (news-medical.net)
  • Recently, several large genome-wide association and linkage studies have identified common genetic variants in more than a dozen loci that appear to contribute to IPF risk. (ersjournals.com)
  • Even if such a risk is small, the allele frequency of the SNP variants is high, and therefore the population attributable risk could be substantial. (biomedcentral.com)
  • Significantly, the rs7927894 variant reported to associate with Crohn disease and atopic dermatitis was found to be in complete linkage disequilibrium with rs7130588 identified by the AAGC studies, and the two predisposing alleles-rs7927894:T and rs7130588:G-occur on the same haplotype. (genengnews.com)
  • GBS is an attractive alternative to array-based methods for generating high volume genome-wide single nucleotide polymorphisms (SNPs) for genome-wide association studies (GWAS) and GS. (frontiersin.org)
  • 0.001 helped the researchers cluster the GWAS-related SNPs into independent SNPs. (news-medical.net)
  • Next, they generated a weighted genetic risk score (GRS) using 129 independent SNPs based on their allelic association with insomnia symptoms in the original GWAS. (news-medical.net)
  • A preliminary case-control GWAS identified 4 SNPs in linkage disequilibrium on chromosome 6 (rs115112393, rs16871327, rs78132896, and rs114504854) that were associated with warfarin-related bleeding in patients of African descent. (medscape.com)
  • Then SpecVar represents genome-wide association studies (GWAS) summary statistics into relevance scores and SNP-associated regulatory subnetworks. (elifesciences.org)
  • SNPs discovered by genome-wide association studies (GWASs) account for only a small fraction of the genetic variation of complex traits in human populations. (nih.gov)
  • CoreSNP is an efficiency way of core marker sets selection based on Genome-wide SNP datasets of crops. (biomedcentral.com)
  • Genome-wide association studies (GWASs) have identified several single-nucleotide polymorphisms (SNPs) to be associated with vitamin D. The aim of this study was to investigate such vitamin D-SNP associations in relation to subsequent breast cancer risk. (biomedcentral.com)
  • The core SNPs were distributed across all chromosomes, exhibiting lower pairwise linkage disequilibrium (LD) and higher polymorphism information content (PIC) and minor allele frequencies (MAF). (biomedcentral.com)
  • We genotyped the two ADIPOQ SNPs in 140 unrelated T2DM patients and 66 nondiabetic controls using the polymerase chain reaction-restriction fragment length polymorphism assay. (who.int)
  • The EGP catalogues single nucleotide variation (also called SNPs) in environmentally-responsive genes in the human genome and carries out research on the biological implications of such genetic variation. (nih.gov)
  • Participants in two independent case-control studies were genotyped for 30 single-nucleotide polymorphisms (SNPs) in the four PGLYRP genes. (nih.gov)
  • Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes. (snpedia.com)
  • A number of single nucleotide polymorphisms (SNPs) within MHC Class I and II genes were found to be associated with variations in the vaccine specific antibody responses and serum levels of immunoglobulins (IgG, IgM) and IgG isotypes (IgG1, IgG4) (all at p (cdc.gov)
  • The pilot/large-scale projects may be for SNPs that are located throughout the genome or that are located in particular genome regions or in sets of genes related to particular processes, organs, or diseases. (nih.gov)
  • Of these mediators, cytokines play a single nucleotide polymorphisms (SNP) in pro-inflammatory cytokine genes and asthma phenotypes (Che et al. (cdc.gov)
  • Because association studies to identify genomic loci associated with particular phenotypic traits have focused primarily on genotyping SNPs, it is important to determine whether common structural polymorphisms are in linkage disequilibrium with common SNPs, and thus can be assessed indirectly in SNP-based studies. (nih.gov)
  • We show that common deletions and SNPs ascertained with similar criteria have essentially the same distribution of linkage disequilibrium with surrounding SNPs, indicating that these polymorphisms may share evolutionary history and that most deletion polymorphisms are effectively assayed by proxy in SNP-based association studies. (nih.gov)
  • Most current methods for inferring ancestry at each locus in the genome use a few thousand single nucleotide polymorphisms (SNPs) that are very different in frequency between West Africans and European Americans, and that are required to not be in linkage disequilibrium in the ancestral populations. (nih.gov)
  • Our study aims to evaluate the joint effect of T2DM associated single nucleotide polymorphisms (SNPs) on the age of onset for T2DM in combination with conventional risk factors (such as sex, body mass index (BMI), and TG/HDL-C ratio) in the Hungarian population. (mdpi.com)
  • Single nucleotide polymorphisms (SNPs) in the peroxisome proliferator-activated receptor ( PPARG ) gene have been associated with cardiovascular risk factors, particularly obesity and diabetes. (hindawi.com)
  • It also offers guides to the use of single nucleotide polymorphisms (SNPs) in association studies. (nhbs.com)
  • We genotyped 12 single-nucleotide polymorphisms (SNPs) distributed over 4.3 kilobases in 296 healthy, unrelated Gambian and Malawian adults. (biomedcentral.com)
  • Alternatively, these TNF SNPs may be serving as neutral markers of functional polymorphisms elsewhere in the central MHC. (biomedcentral.com)
  • A disintegrin and metalloprotease 33 ( ADAM33 ) has been identified as a susceptibility gene for asthma and single nucleotide polymorphisms (SNPs) in this gene have been associated with excessive decline of lung function in individuals with asthma. (atsjournals.org)
  • In this study, we have investigated the role of eight single nucleotide polymorphisms (SNPs) in the ADAM33 gene in lung function decline in 1,390 subjects of the Vlagtwedde-Vlaardingen cohort. (atsjournals.org)
  • Approximately 50% of the variability in warfarin dose requirement is attibuted to common single nucleotide polymorphisms (SNPs). (medscape.com)
  • Three single nucleotide polymorphisms (SNPs), 2 in the CYP2C9 gene and 1 in the VKORC1 gene, have been found to play key roles in determining the effect of warfarin therapy on coagulation. (medscape.com)
  • First, we characterized the linkage disequilibrium within the PPARalpha gene in an initial case-control sample of 806 individuals from the Regensburg Myocardial Infarction Family Study using a panel of densely spaced SNPs (single nucleotide polymorphisms) across the gene. (tum.de)
  • n = 2,893 Hispanic/Native Americans (H/NA) and Mexico ( n = 1,810), we examined influence of 25 CYP19A1 tagging single-nucleotide polymorphisms (SNPs) on breast cancer risk and mortality, considering NA ancestry. (cdc.gov)
  • Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. (nordiag.com)
  • Allele frequencies for each SNP are listed in Table 1 . (biomedcentral.com)
  • In the VKORC1 1639 (or 3673) SNP, the common G allele is replaced by the A allele. (medscape.com)
  • A total of 391 Mb of scaffolds (89% of the estimated 440-Mb genome) was assembled into 14 chromosomal linkage groups via an ultra-high-density genomic linkage map consisting of 3.4 million markers (Fig. 1 and Supplementary Note ). (nature.com)
  • In this study we genotyped over 40,000 SNPs to characterize the spatial distribution of genomic variation for G. capensis throughout its core distribution. (frontiersin.org)
  • Results suggest that fish sampled at the northernmost range (off central Namibia) are characterized by lower genomic diversity, although the region exhibited the highest number of private SNPs, suggesting some degree of geographic isolation. (frontiersin.org)
  • Genomic approaches for the genetic dissection of complex diseases: Linkage disequilibrium mapping. (uninsubria.eu)
  • As a consequence, a large proportion of TNF SNPs must be typed to detect a disease-modifying SNP at this locus. (biomedcentral.com)
  • In order to understand, first, how the TNF SNPs relate to each other, and second, which SNPs are the best markers of the TNF locus in general, we applied two new analytical techniques to our haplotypic data. (biomedcentral.com)
  • The second technique, entropy maximization method (EMM), selects those SNPs that most effectively dissect the underlying haplotypic structure of a locus. (biomedcentral.com)
  • The 11q13.5 locus, meanwhile, is located near an SNP recently reported to associate with the immune-related disorders, Crohn disease and atopic dermatitis, the team continues. (genengnews.com)
  • Theoretical basis of linkage analysis in humans (LOD scores). (uninsubria.eu)
  • Here we present panels of about 4,300 ancestry informative markers (AIMs) that are subsets respectively of SNPs on the Illumina 1 M, Illumina 650, Illumina 610, Affymetrix 6.0 and Affymetrix 5.0 arrays. (nih.gov)
  • For family-based data, most existing tests for interaction depend on the assumption that the markers are in linkage equilibrium. (nih.gov)
  • Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. (bas.ac.uk)
  • AEA revealed that many SNPs in TNF are poor markers of each other. (biomedcentral.com)
  • While the genetic effect in the 5' block seems to be secondary to differences in promoter activation due to SNP g.-11391G→A, [ 69 ] the situation is more complex for the 3' block where the marker displaying association with metabolic traits (i.e. (medscape.com)
  • Analyses were extended to linkage disequilibrium (LD) based haplotypes. (bmj.com)
  • The results of these analyses allow us to prioritize SNPs for genotyping in future disease-association studies. (biomedcentral.com)
  • Logistic regression analyses yielding ORs with 95% CIs were performed to investigate selected SNPs in relation to low levels of vitamin D (below median) as well as to the risk of breast cancer. (biomedcentral.com)
  • Results from stratified analyses showed diverse associations with breast cancer risk for a few of the tested SNPs, depending on whether vitamin D level was high or low. (biomedcentral.com)
  • Prior investigations have analyzed the relationship between common PPARG SNPs and various metabolic disorders. (hindawi.com)
  • ABSTRACT This study aimed to estimate the frequency of the SNPs (+45T>G and +276G>T) genotypes and investigate the association between the two SNPs and adiponectin concentration, metabolic parameters and risk of T2DM in the Bahraini population. (who.int)
  • There was no association between both SNPs and metabolic parameters. (who.int)
  • To pursue the causal origin of these TNF disease associations we must begin with a detailed understanding of the allelic associations between different TNF SNPs. (biomedcentral.com)
  • This prior work, together with the AAGC results, "suggest that rs4129267, or a causal variant in linkage disequilibrium with it, increases the risk of development of asthma by upregulating protein concentrations of sIL-6R or membrane-bound IL-6R, or both, which in turn contributes to the development and maintenance of a Th2 immune response in the lung," they conclude. (genengnews.com)
  • To assess whether SNPs in ADAM33 are associated with accelerated lung function loss in the general population and with chronic obstructive pulmonary disease (COPD). (atsjournals.org)
  • We demonstrated that SNPs in ADAM33 are associated with accelerated lung function decline in the general population. (atsjournals.org)
  • We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula , as well as seven other members of Betulaceae. (nature.com)
  • The availability of a dense collection of SNPs will stimulate many areas of biological research, including the identification of the genetic components of disease. (nih.gov)
  • Illumina array: 2.5M SNPs incl. (who.int)
  • The effect of the 3' block, captured by SNP g.+276, is especially strong for insulin resistance and CAD, whereas it is only marginally significant for adiponectin levels. (medscape.com)
  • For instance, SNP g.-11391G→A displays the strongest association with adiponectin levels, yet it does not seem to be associated with type 2 diabetes or CAD. (medscape.com)
  • Conversely, SNP g.+276 shows a rather weak association with adiponectin levels, yet it appears to have a strong effect on the risk of insulin resistance and CAD. (medscape.com)
  • Thus, studies considering the impact of SNPs on adiponectin production (determined for instance by measuring adiponectin expression in adipocytes) rather than its serum concentrations may be more revealing. (medscape.com)
  • Linkage disequilibrium analysis identified the presence of 17 SNPs in high linkage with the Sr38 -specific marker. (unl.edu)
  • These SNPs potentially tagging the Sr38 gene could be used in marker-assisted selection after validating them in additional genetic backgrounds. (unl.edu)
  • However, selecting minimal marker sets from large-scale SNP dataset can be challenging to distinguish a maximum number of samples. (biomedcentral.com)
  • Combining functional and linkage disequilibrium information in the selection of tag SNPs. (vldb.org)
  • Linkage disequilibrium patterns and functional annotations showed that significant SNPs were strongly correlated with other functional regulatory SNPs. (cdc.gov)
  • One SNP failed the assay, and three had little to no variation. (nih.gov)
  • In this study, 86,604 SNPs were tested for association with BMI, and at least two genetic models were considered, including a recessive mode of inheritance. (cdc.gov)
  • Therefore, the goal of the present study was to explore the association between 4 PPARG SNPs, including the Pro12Ala SNP, and CHD risk in two independent studies among white subjects. (hindawi.com)
  • Linkage disequilibrium plot of five SLC1A3 SNPs in 813 study participants. (molvis.org)
  • The aim of the present study was to investigate breast cancer risk in relation to SNPs previously identified in GWASs on vitamin D levels and related phenotypes. (biomedcentral.com)
  • The present study was a prospective, nested case-control study with information on SNPs, vitamin D levels and subsequent breast cancer. (biomedcentral.com)
  • Twenty-three SNPs were tested on how they are associated with the age of onset for T2DM in the Case population and 12 of them with a certified effect on the age of T2DM onset were chosen for an optimized genetic risk score (GRS) analysis. (mdpi.com)
  • SNPs previously associated with vitamin D in GWASs were identified. (biomedcentral.com)
  • Researchers investigating vitamin D-related SNPs and breast cancer risk have focused mainly on SNPs located in the vitamin D receptor (VDR) gene. (biomedcentral.com)
  • We used online SNP function prediction tools to screen the candidate SNPs that might be associated with the regulation of the ARHGEF18 expression. (hindawi.com)
  • The first, association efficiency analysis (AEA), precisely defines the ability of one SNP to detect association at every other SNP in a case-control scenario. (biomedcentral.com)
  • These SNPs are also risk factors for COPD. (atsjournals.org)
  • Heterozygotes of one SNP ( rs12239582 ) were found to have a statistically significant association with a low risk of breast cancer (OR 0.82, 95% CI 0.68-0.99), and minor homozygotes of the same SNP were found to have a tendency towards a low risk of being in the group with low vitamin D levels (OR 0.72, 95% CI 0.52-1.00). (biomedcentral.com)
  • SNPs associated with vitamin D may also be associated with the risk of breast cancer. (biomedcentral.com)
  • After multiple comparison adjustment, none of the SNPs were significantly associated with breast cancer risk or mortality. (cdc.gov)
  • Two SNPs remained significantly associated with increased breast cancer risk in women of moderate to high NA ancestry (≥29 %): rs700518, OR GG 1.36, 95 % CI 1.11-1.67 and rs11856927, OR GG 1.35, 95 % CI 1.05-1.72. (cdc.gov)
  • b ) For a single phenotype, SpecVar can use relevance score and SNP-associated regulatory subnetworks to identify and interpret relevant tissues. (elifesciences.org)
  • The most significant SNP, rs7566605, had an unadjusted p-value of 0.0026, which was claimed to reach overall significance. (cdc.gov)
  • Individual SNP tests also showed nominally significant associations with odds ratios of between 1.34 and 3.78, depending on the SNP and genetic model. (nih.gov)
  • The majority of SNPs previously associated with levels of vitamin D showed a statistically significant association with circulating vitamin D levels. (biomedcentral.com)
  • Single SNP analysis showed significant association with the disease phenotype [OR (odds ratio)=0.74, P=0.012, 95% CI (confidence interval)=0.61-0.94 for rs135551]. (tum.de)
  • and the entropy maximization method (EMM), which selects the subset of SNPs that most effectively dissects the underlying haplotypic structure. (biomedcentral.com)
  • In addition, the core SNPs capture a certain level of the original population structure. (biomedcentral.com)
  • Primer: SNP-associated studies and what they can teach us. (nih.gov)
  • Large collaborative studies including thousands of individuals from a few different ethnic groups, recruited and phenotyped according to standard protocols and genotyped for the same set of SNPs, are clearly needed to conclusively address this matter. (medscape.com)
  • We assessed the relationship between 4 PPARG SNPs (C-681G, C-689T, Pro12Ala, and C1431T) and coronary heart disease (CHD) in the PRIME (249 cases/494 controls, only men) and ADVANCE (1,076 cases/805 controls, men or women) studies. (hindawi.com)
  • Early studies analyzed the association between the PPARG Pro12Ala SNP and coronary heart disease (CHD) in cohorts from North America. (hindawi.com)
  • Modern SNP arrays provide data on hundreds of thousands of SNPs per sample, and to use these to infer ancestry, using many of the standard methods, it is necessary to choose subsets of the SNPs for analysis. (nih.gov)
  • Clustering of SNP Data with Application to Genomics. (vldb.org)
  • Twelve SNPs spanning 4.3 kb (Figure 1 ) were genotyped in 212 Gambian and 84 Malawian adults with no missing data. (biomedcentral.com)
  • We show that 45% of variance can be explained by considering all SNPs simultaneously. (nih.gov)
  • To validate the usefulness of these panels, we applied them to samples that are different from the ones used to select the SNPs. (nih.gov)
  • The continuous advancements in high-throughput sequencing technology have facilitated the generation of a large number of SNPs. (biomedcentral.com)
  • CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs. (vldb.org)
  • Differences in prevalence of SNPs were analyzed with χ 2 tests. (atsjournals.org)
  • None of these SNPs show strong evidence of association with BMI. (cdc.gov)