• Based on RNA-seq data, SNPs were identified and genotyped using PCR-RFLP or PCR-HRM methods in 254 Arabian horses that competed in flat races. (biomedcentral.com)
  • Genotypes of three single nucleotide polymorphisms (SNPs) of LOXL1 (rs1048661, rs3825942, and rs2165241) were analyzed with direct sequencing, and a case-control association study was performed. (molvis.org)
  • There was no significant association between the genotype frequencies of the three SNPs and the XFS phenotypes. (molvis.org)
  • The risk alleles of these SNPs were similar to those of other Asian populations, such as Japanese or Chinese, but differed from non-Asian populations, suggesting that still unidentified genetic or environmental factors may contribute to disease expression. (molvis.org)
  • High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. (biomedcentral.com)
  • From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. (biomedcentral.com)
  • It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats. (biomedcentral.com)
  • Given standard multiple sequence alignments, Illumina chip genotyping data or Sanger sequencing traces as input, SNiPlay detects SNPs and indels events. (biomedcentral.com)
  • The risk of BC was not found significantly associated with exposure to PCBs and OCPs, regardless of genotype for all investigated SNPs. (biomedcentral.com)
  • Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. (biomedcentral.com)
  • Seven single-nucleotide polymorphisms (SNPs) were analyzed in 500 histopathologically confirmed oral cancer samples and 500 long-term tobacco users (LTTUs) as controls using allelic discrimination real-time polymerase chain reaction or high-resolution melting analysis. (brjnmims.org)
  • For example, SNPs identified by high-throughput sequencing serve as markers of the associations between genotypes and phenotypes ( Hudson, 2008 ). (ashs.org)
  • 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)
  • 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)
  • It is noteworthy that no differences in genotype frequencies of the VDBP polymorphisms were associated with serum VDBP levels or between type 1 diabetic patients and control subjects. (diabetesjournals.org)
  • 2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. (biomedcentral.com)
  • In a second round, it sends sequences and genotyping data into an integrative pipeline executing a series of modules in charge of various types of post-processing of the collected polymorphisms and associated genotyping data. (biomedcentral.com)
  • rs10046) and CYP19A1 ((TTTA)n repeats) polymorphisms and BRCA1 founder mutation using TaqMan allelic discrimination method and polymerase chain reaction based restriction fragment length polymorphism. (biomedcentral.com)
  • From 189 healthy volunteers who were genotyped for CYP2C9 polymorphisms, 11 control subjects ( CYP2C9 * 1/ * 1 ), 9 heterozygous and 2 homozygous for the CYP2C9 * 3 allele participated in the pharmacokinetic drug interaction study. (aspetjournals.org)
  • in individuals of the CYP2C9 * 1/ * 1, * 1/ * 3 , and * 3/ * 3 genotypes to characterize the magnitude of the drug interaction in subjects with different CYP2C9 polymorphisms. (aspetjournals.org)
  • Regulatory polymorphisms in cis-acting elements result in the unequal expression of alleles. (springer.com)
  • We aimed to perform a more extensive evaluation of differential allelic expression between blood and breast in order to assess the potential usefulness of LCL and fresh blood in association studies, to identify regulatory polymorphisms related to susceptibility to breast cancer. (springer.com)
  • Three polymorphisms (i.e., rs9588884, rs982873 and rs1813389) in the promoter of miR-17-92 were analyzed among 874 cases and 1132 controls using a TaqMan allelic discrimination assay or a polymerase chain reaction-restriction fragment length polymorphism method. (oncotarget.com)
  • The frequency of these polymorphisms differs among ethnic populations (8). (123dok.net)
  • Both branches use the frequencies of different alleles of a gene in breeding populations (gamodemes), and combine them with concepts from simple Mendelian inheritance to analyze inheritance patterns across generations and descendant lines. (wikipedia.org)
  • New River drainage populations exhibited the southern allele at high frequency, suggesting their historic native character as southern, with presence of northern alleles due to stocking or stream capture events. (intechopen.com)
  • Following data filtering and quality checks to remove missing data, 220 sequences were retained and analysed for the allele frequency spectrum, genetic diversity both within the host and between populations and signatures of selection. (biomedcentral.com)
  • The low frequencies of the Pfcsp vaccine haplotype in the analysed populations indicate a need for additional molecular and immuno-epidemiological studies with broader temporal and geographic sampling in endemic populations targeted for RTS,S application. (biomedcentral.com)
  • The T allele at rs1048661 (odds ratio [OR]=14.29, 95% confidence interval [CI]=6.25-33.3) and the C allele at rs2165241 (OR=7.14, 95% CI=1.59-33.3) were risk alleles in Korean subjects, which was consistent with findings in other Asian populations. (molvis.org)
  • However, our findings were opposite to results from Caucasian populations in which the risk alleles at rs1048661 and rs2165241 were G and T, respectively. (molvis.org)
  • For example, the risk allele of rs1048661 has been reported to be different between Asian and Caucasian populations. (molvis.org)
  • In Indian [ 21 ] and Chinese [ 18 ] populations, the G allele of SNP rs1048661 was not associated with XFS/XFG. (molvis.org)
  • For example, interactions between alleles, that are not transmitted in panmictic populations, and epigenetic variants, that are non-mendelian inherited, contribute to the total phenotypic variation but may result in decreased heritability [ 5 ]. (biomedcentral.com)
  • We found pronounced ethnic differences in NAT2 genotypes with yet unknown effect on the health risks for environmental or occupational exposures in minority populations. (aacrjournals.org)
  • The study revealed no association between CYP19/PvuII genotype and cystic ovarian disease in HF crossbred populations but 'AG' genotype of ER1 gene is associated with higher incidence of COD. (ijlr.org)
  • For this purpose, we genotyped exon2, exon5 ( C540T and C588T ), exon7 ( T813C ), exon8 ( K289M ), and exon9 of GABRG2 gene by restriction fragment length polymorphism and Sanger's sequencing in 87 drug-responsive idiopathic generalized epilepsy patients, 55 drug-resistant epilepsy patients, and 83 healthy controls. (hindawi.com)
  • The genotypes were elucidated by polymerase chain reaction-restriction fragment length polymorphism followed by DNA sequencing. (bvsalud.org)
  • The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. (biomedcentral.com)
  • Distribution of genotypes of polymorphism Arg16Gly was different relative to body mass index (χ 2 = 9.797;p = 0.04). (biomedcentral.com)
  • Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since 'universal' barcodes can lack resolution at the local scale. (biomedcentral.com)
  • Commonly, the frequency of the allele causing "more" in the phenotype (including dominance) is given the symbol p, while the frequency of the contrasting allele is q. (wikipedia.org)
  • Referenced article focusing on the relationship between phenotype and genotype. (cancerindex.org)
  • We could not identify a significant phenotype-genotype correlation. (biomedcentral.com)
  • The enormous variants and mutations found mean that we are still far from being able to concretely clarify a genotype-phenotype relationship. (bvsalud.org)
  • In diploid organisms, the average genotypic "value" (locus value) may be defined by the allele "effect" together with a dominance effect, and also by how genes interact with genes at other loci (epistasis). (wikipedia.org)
  • The number of alleles per locus ranged from two to six, with a mean value of 2.85 alleles per locus. (biomedcentral.com)
  • Each individual is found to harbor as many as 600 OR allelic variants, ~50% higher than the locus count. (biomedcentral.com)
  • From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56-7586) per locus across genotyped samples. (biomedcentral.com)
  • Allelic and genotypic frequencies of NOD2/CARD15 variations were calculated in patients and matched with those of 25 healthy controls. (biomedcentral.com)
  • CI = 1.2-13.5) but not for genotypic frequencies. (biomedcentral.com)
  • Differential allelic expression ratios were determined by Taqman assay. (springer.com)
  • These distances can be used for the calculation of clonal diversity statistics or used for further analysis in R. Allelic diversity statistics and Polymorphic Information Content are also available. (rediris.es)
  • The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. (biomedcentral.com)
  • Polymorphic variants at regulatory elements can cause differential allelic expression (DAE), thus using DAE as a quantitative trait could help identify such variation. (springer.com)
  • Due to the continuous distribution of phenotypic values, quantitative genetics must employ many other statistical methods (such as the effect size, the mean and the variance) to link phenotypes (attributes) to genotypes. (wikipedia.org)
  • Genotype frequencies of each SNP were compared according to the XFS phenotypes. (molvis.org)
  • A widely accepted working hypothesis is that allelic variants of OR genes may harbor different functional characteristics and hence, may generate different odorant sensitivity phenotypes in different members of the human population [ 16 - 18 ]. (biomedcentral.com)
  • In patients harboring alleles Gly16 and Glu27, previoulsy associated with increased down regulation of beta-2 adrenergic receptors, a statistically significant difference relative to prognosis has not been demonstrated. (biomedcentral.com)
  • Genetic analysis may demonstrate a number of allelic mutations in the pseudocholinesterase gene, including point mutations resulting in abnormal enzyme structure and function and frameshift or stop codon mutations resulting in absent enzyme synthesis. (medscape.com)
  • In the haplotype analysis, the T-G-C haplotype composed of all three risk alleles was significantly overrepresented in XFS and conferred an 11.36 fold (95% CI=5.97-23.49) increased likelihood of XFS. (molvis.org)
  • Allele and haplotype analysis also did not disclose any significant difference regarding mortality. (biomedcentral.com)
  • Data from the Exome Aggregate Consortium (ExAC) allows a Bayesian approach to calculate penetrance, in that population frequencies of pathogenic germline variants should be inversely proportional to their penetrance for disease. (bmj.com)
  • Penetrance of pathogenic SDHA-C variants was calculated by comparing allelic frequencies in cases versus controls from ExAC (removing those variants contributed by The Cancer Genome Atlas). (bmj.com)
  • To date, 30 CYP2C9 allelic variants located within the coding region have been reported ( http://www.imm.ki.SE/CYPalleles ). (aspetjournals.org)
  • To facilitate future exploration and testing of PMS2 variants, we share the raw and processed LR-PCR data from commercially available cell lines, as well as variant frequencies from a diverse patient cohort. (biomedcentral.com)
  • Some exact haplotypes (CCG and CCA) of the VDR gene may act as low penetrance alleles in inclination to GC. (bvsalud.org)
  • In single gene disorders (as opposed to multifactorial-complex disorders), the mutation's population frequency is low, its penetrance is high, and the contribution of environment is lower with notable exceptions of PKU and few others. (dorak.info)
  • The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. (biomedcentral.com)
  • To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. (biomedcentral.com)
  • There are more than 80 unique alleles that have been described for the CYP2D6 enzyme, 5 and the different allele combinations yield phenotypic diversity in the general population. (ahdbonline.com)
  • Additive variance instead designates the effect of an allele as measured by its average deviation from the population phenotypic mean. (biomedcentral.com)
  • Multiple non-exclusive hypotheses have been proposed to resolve this paradox among which an excess of rare alleles limiting detection power [ 9 ], and a prominence of undetectable epistatic interactions that could significantly contribute to phenotypic variation [ 6 ]. (biomedcentral.com)
  • however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. (biomedcentral.com)
  • No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. (biomedcentral.com)
  • Precise editing is complicated further because two copies of somatic alleles are present in the diploid genome. (nature.com)
  • SNP assays directly interrogate the sequence variation, reducing genotyping errors compared to assays based on size discrimination or hybridization. (biomedcentral.com)
  • Overall the probability of survival was not significantly predicted by genotypes of Gln27Glu, Arg16Gly, or Thr164Ile. (biomedcentral.com)
  • The miRNA-146a rs2910164 mutation significantly reduced the risk of cervical cancer in both recessive model (OR= 0.804, 95%CI= 0.652-0.992, P = 0.042;CC vs. CG+GG) and allelic model (OR= 0.845, 95%CI= 0.721-0.991, P = 0.038;C vs. G). There was no significant correlation between miRNA -499 rs3746444 and the risk of cervical cancer. (researchsquare.com)
  • Carriers of the ancestral T allele ( n = 44) have significantly lower resting and exercise hypoxic ventilatory responses than C/C homozygous carriers ( n = 40). (frontiersin.org)
  • On stratification, IL-10 (-1082 A/G) was significantly associated with hepatocellular carcinoma risk in the non-Asian population under dominant (OR: 0.62, 95% CI: 0.45-0.86, 4 studies), heterozygous (OR: 0.60, 95% CI: 0.43-0.85) and allelic models (OR: 0.79, 95% CI: 0.64-0.99). (biomedcentral.com)
  • Differential allelic expression (DAE) in heterozygote individuals could be used to develop a new approach to discover regulatory breast cancer susceptibility loci. (springer.com)
  • Inbreeding increases the expression of recessive traits due to more heterozygous carriers mating with each other. (varsitytutors.com)
  • These results confirm that carriers exhibit hypo-sensitivity to exogenous FSH during COS, documenting that the frequency of v-betaLH in Denmark is similar to a number of European countries. (biomedcentral.com)
  • Our study shows that carriers of the T allele have a higher risk of SHAI than carriers of the mutated C/C genotype. (frontiersin.org)
  • The results revealed that the 13 pairs of primers used amplified a total of 37 alleles in the accessions studied. (biomedcentral.com)
  • Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. (biomedcentral.com)
  • A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. (rediris.es)
  • Functions are also included for assigning alleles to isoloci in cases where one pair of microsatellite primers amplifies alleles from two or more independently segregating isoloci. (rediris.es)
  • In a population that is in Hardy-Weinberg equilibrium, the frequency of homozygous dominant individuals is 0.36. (varsitytutors.com)
  • The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. (biomedcentral.com)
  • Alive female mosquitoes were genotyped for various resistance markers at different time points post-exposure to evaluate the impact of insecticide resistance on the efficacy of bednets. (biomedcentral.com)
  • Recent advances in genotyping technologies have made it possible to create genetic maps and exploit genetic linkage between markers and traits with unprecedented resolution. (ashs.org)
  • Cell-surface receptors are often characterized by several haplotypic alleles in the population, sometimes with different functional properties. (biomedcentral.com)
  • The aim of this study was to confirm the hypothesis that women with v-betaLH display hypo-sensitivity to exogenous FSH in a larger IVF population and to explore the frequency of this variant in a Danish female population. (biomedcentral.com)
  • The study population was divided into two groups according to their LH genotype. (biomedcentral.com)
  • The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. (biomedcentral.com)
  • The allele frequency was 3.5% in the normal Tunisian population. (who.int)
  • The subjects were un- ers of the factor V 1691A allele have been related to the patients and were taken to shown to have an increased risk for venous represent the general Tunisian population. (who.int)
  • Information is lacking about the benefits and risks of genetic testing, the efficacy of early interventions, and the population distribution of genotypes and other risk factors associated with disease conditions. (cdc.gov)
  • The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. (biomedcentral.com)
  • Significant differences are present between COMT genotypes for oxygen saturation and ventilatory responses to hypoxia at rest. (frontiersin.org)
  • We show that differential allelic expression is common among these 12 candidate genes and is comparable between breast and blood (fresh and transformed lymphoblasts) in a significant proportion of them. (springer.com)
  • The allelic information in the linkage panel will be a significant resource for both tomato genetics and future breeding approaches. (ashs.org)
  • Overall, the heterozygous model showed a marginal significant association only between IL-10 (-1082 A/G) and hepatocellular carcinoma risk (OR: 0.82, 95% CI: 0.67-1.00, 9 studies). (biomedcentral.com)
  • There was no significant difference in allele and genotype frequencies of +276G>T between type T2DM patients and controls. (who.int)
  • Most clinically significant causes of pseudocholinesterase deficiency are due to one or more inherited abnormal alleles that code for the synthesis of the enzyme. (medscape.com)
  • The differential frequencies in oral cancer and LTTUs were calculated using SPSS software (version 19), and odds ratio (OR) to indicate risk to oral cancer using Hutchon.net. (brjnmims.org)
  • Our findings support the use of differential allelic expression in blood as a surrogate for breast tissue in future studies on predisposition to breast cancer. (springer.com)
  • In the current study, flurbiprofen was used as a probe substrate and fluconazole as a prototypical inhibitor to investigate whether genotype-dependent inhibition of CYP2C9 occurs in vivo. (aspetjournals.org)
  • iii) investigate the contribution of non allelic interactions. (biomedcentral.com)
  • Here, we examined whether serum levels or genotypes of the vitamin D-binding protein (VDBP), a molecule key to the biologic actions of vitamin D, specifically associate with the disorder. (diabetesjournals.org)
  • The rare G allele of +45T>G occurred more frequently than the common T allele in T2DM patients compared with controls, and was associated with lower serum adiponectin levels. (who.int)
  • This method uses unlabeled primers and interrogates the entire amplicon, providing an efficient SNP genotyping system in terms of reagent cost, throughput, and data production. (biomedcentral.com)
  • The different distribution of genotypes depending on race distance indicated the possibility of using a SNP in the SLC16A1 gene as a marker to predict the best race distance for a horse. (biomedcentral.com)
  • The gene effects (above) provide the framework for quantities: and the frequencies of the contrasting alleles in the fertilization gamete-pool provide the information on occurrences. (wikipedia.org)
  • This ensures that coincidental occurrences do not drastically alter allelic frequencies. (varsitytutors.com)
  • These grapevine projects are based on the present ability to obtain high-throughput sequences and subsequent SNP genotypes using the recently available complete genomic sequence. (biomedcentral.com)
  • The subsequent mathematical development also implied that the frequency distribution within the effective gamete-pool was uniform: there were no local perturbations where p and q varied. (wikipedia.org)
  • In a study of 259 patients with ischemic or idiopathic dilated cardiomyopathy, prognosis was less favorable in patients harboring the allele Ile164 relative to patients harboring the allele Thr164. (biomedcentral.com)
  • A total of 189 healthy subjects were enrolled in the genotype screening phase of the study. (aspetjournals.org)
  • Hepatocellular Carcinomas from Iran: Evidence study of lung cancer among European asphalt carcinoma among postmenopausal women in the for Lack of Association between HBV Genotype workers. (who.int)
  • Results: The frequency of Fok1 genotypes (TC and TT) was found higher in GC cases compared to controls (P ≤ 0.05). (bvsalud.org)
  • These results have implications for the efficacy of the vaccine in Ghana and will inform the choice of alleles to be included in future multivalent or chimeric vaccines. (biomedcentral.com)
  • At the rs3825942, the G allele (OR=12.50, 95% CI=2.94-50.0) was a risk allele for XFS, which was similar to results from most other ethnic groups except black South Africans in whom the A allele increased the risk. (molvis.org)
  • Ultrarapid metabolizers (UMs): individuals who have multiple copies of a functional allele and/or an allele with a promoter mutation and show increased enzyme activity. (ahdbonline.com)
  • These abnormal alleles may result in a failure to produce normal amounts of the enzyme or in production of abnormal forms of pseudocholinesterase with altered structure and lacking full enzymatic function, as described below. (medscape.com)
  • The approach, called genotyping by sequencing (GBS), can be applied to species with high diversity and large genomes such as maize. (biomedcentral.com)
  • These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes. (biomedcentral.com)
  • In summary, this meta-analysis shows that the mutant genotypes of miRNA -146a rs2910164 and miRNA -196a2 rs11614913 are associated with a reduced risk of cervical cancer. (researchsquare.com)
  • In addition, SNP analysis of a second sample set of banked DNA samples from 1,502 type 1 diabetic patients and 1,880 control subjects also was used to determine genotype frequencies. (diabetesjournals.org)
  • Nous avons génotypé les deux polymorphismes mononucléotidiques du gène ADIPOQ chez 140 patients atteints de DNID sans lien de parenté et 66 témoins non diabétiques en recourant à l'analyse du polymorphisme de longueur des fragments de restriction par réaction en chaîne de polymérase. (who.int)
  • Elucidation of the molecular epidemiology of TcV and TcVI has been complicated by limited sample collections and difficulties distinguishing these genotypes from their parental DTUs ( 6 ) and each other ( 7 ). (cdc.gov)
  • Previous in vitro work has demonstrated that genotype-dependent inhibition of CYP2C9 mediated flurbiprofen metabolism, suggesting the possibility of genotype-dependent inhibition interactions in vivo. (aspetjournals.org)
  • Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. (biomedcentral.com)
  • Among the descriptive data, the allele frequency of the C282Y variant (0.252) stands out, which differs from the national scenario. (scielo.br)
  • The frequency of the Greenlandic founder mutation in BRCA1 was as expected higher in cases than in controls. (biomedcentral.com)
  • In a minority of regions, however, standard NGS strategies that use hybridization to capture and sequence short DNA fragments could incorrectly identify genotypes. (biomedcentral.com)
  • however, the genetic map for the large-fruited fresh-market tomato ( Solanum lycopersicum ) has never been constructed, and the recombination frequency between DNA fragments is only partly understood for fresh-market tomato. (ashs.org)
  • It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model, with or without taking ploidies and allele frequencies into account. (rediris.es)
  • these individuals show an increased frequency of CYP2D6*3, CYP2D6*4, CYP2D6*5, or CYP2D6*6 genetic alterations. (ahdbonline.com)
  • This is the "allele" effect mentioned above. (wikipedia.org)
  • Genotypes were stratified according to deleterious effect of C282Y variant. (scielo.br)
  • Additionally, the rare allele of rs9588884 G and the rs982873 C revealed a reduced luciferase activity. (oncotarget.com)
  • Other reports from Japan [ 16 , 17 , 20 , 22 ] and China [ 15 ] demonstrated that the opposite T allele of SNP rs1048661 increased the risk for XFS. (molvis.org)