• Body S11 TRBV gene use based on the TRBV7-2 genotype in DS3. (findadig.com)
  • The code for the analyses as well as the results are obtainable in the Github repository (www.github.com/omaviv/TCR_genotype) [78]. (findadig.com)
  • For repertoire analyses from the four data models, as well as the sequences from the undocumented alleles inferred, please make reference to www.github.com/omaviv/TCR_genotype/tree/master/figures/data. (findadig.com)
  • SOLUTIONS TO confront this problem, AIRR-seq-based strategies have already been created for B cells lately, allowing haplotype and genotype inference and discovery of undocumented alleles. (findadig.com)
  • Here, we modified a B cell pipeline for undocumented alleles, genotype, and haplotype inference for complete and incomplete AIRR-seq TCR data models. (findadig.com)
  • Methods The genotype of nine SNPs in the FP receptor gene was determined by direct DNA sequencing, or other techniques, in 82 patients with glaucoma or OH who were treated with latanoprost monotherapy in one eye. (bmj.com)
  • The CD36 rs1334512 (-53) T allele as well as the TT genotype associated with protection from severe disease (severe versus control, TT versus GG, OR = 0.37, P = 0.004). (biomedcentral.com)
  • There was no significant difference in allele and genotype frequencies of +276G>T between type T2DM patients and controls. (who.int)
  • Aim To examine whether intraocular pressure (IOP) reduction by latanoprost correlates with single nucleotide polymorphisms (SNPs) of the prostaglandin F2α (FP) receptor gene in patients with glaucoma and ocular hypertension (OH). (bmj.com)
  • The correlation between %ΔIOP and SNPs in the FP receptor gene was analysed. (bmj.com)
  • Conclusions An association was found between SNPs of the FP receptor gene and the response to latanoprost in patients with glaucoma or OH. (bmj.com)
  • The aim of this study was to investigate the association of SNPs of three adhesion molecule genes, ICAM1 , PECAM1 and CD36 , with severity of falciparum malaria in a malaria-endemic and a non-endemic region of India. (biomedcentral.com)
  • Single nucleotide polymorphisms (SNPs) in genes encoding CD36, ICAM-1 and PECAM-1 have been previously correlated with disease protection/susceptibility from different populations but these reports have often been contradictory. (biomedcentral.com)
  • We investigated the association of single-nucleotide polymorphisms (SNPs) and haplotypes in EPHB4 with risk of ICH at clinical presentation in patients with BAVM. (kaiserpermanente.org)
  • METHODS AND RESULTS: Eight haplotype-tagging SNPs spanning approximately 29 kb were tested for association with ICH presentation in 146 white patients with BAVM (phase I: 56 ICH, 90 non-ICH) using allelic, haplotypic, and principal components analysis. (kaiserpermanente.org)
  • In principal components analysis, 2 components explained 91% of the variance and complemented haplotype results by implicating 4 SNPs at the 5′ end, including rs314308 and rs314313. (kaiserpermanente.org)
  • 5.0 × 10 −6 ) of SNPs annotated to four genes. (frontiersin.org)
  • Genetic polymorphisms in CYP1A1, CYP1B1, COMT, GSTP1 and NAT2 genes and association with bladder cancer risk in a French cohort. (cdc.gov)
  • Beta-2 adrenergic receptor gene polymorphisms Gln27Glu, Arg16Gly and Thr164Ile were suggested to have an effect in heart failure. (biomedcentral.com)
  • In this study sample, we were not able to demonstrate an overall influence of polymorphisms Gln27Glu and Arg16Gly of beta-2 receptor gene on prognosis. (biomedcentral.com)
  • These findings substantiate the hypotheses that polymorphisms Arg16Gly, Gln27Glu and Thr164Ile of beta-2 receptor gene might be functional and might be associated with differences in the survival rate of patients with heart failure. (biomedcentral.com)
  • We performed this study to evaluate the polymorphisms Gln27Glu, Arg16Gly, and Thr164Ile of the beta-2 receptor gene relative to demographic and clinical variables, as well as, survival rate in a series of patients with heart failure of different etiologies. (biomedcentral.com)
  • The fasting blood samples were collected and VDR polymorphisms were detected using TaqMan fluorescent probes, and the three sites of BsmI-ApaI-TaqI were subjected to haplotype analysis. (hindawi.com)
  • Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions. (lu.se)
  • Allele frequencies for each Y-STR locus in pooled sample and estimated value of gene diversity (GD) were evaluated. (nih.gov)
  • the average population still shows a mean of 6.86 alleles per locus compared to a mean of 7.80-8.93 for nonisolated populations. (bioone.org)
  • GWAS was performed using haplotype reference consortium(HRC)-imputed genotypes of common variants in 3,514 individuals from the first and 2,076 individuals from the second cohort of the Rotterdam Study. (frontiersin.org)
  • Based on these previous analyses and clinical findings, CLRN1 was directly sequenced in 17 patients susceptible to carrying mutations in this gene. (molvis.org)
  • Germline loss of function mutations followed by somatic loss of non-mutant alleles in the tumours 2- 4 suggests a tumour suppressor role for mitochondrial complex II in the paraganglia. (bmj.com)
  • 3, 10 However, analyses of SDHC in four series of patients with paraganglioma or pheochromocytoma 6, 8, 11, 12 yielded no definitive SDHC mutations. (bmj.com)
  • Mutations in the CYP1B1 gene may contribute to juvenile-onset open-angle glaucoma. (cdc.gov)
  • The close genomic locations of these two genes as well as their functional similarity have hindered efforts to define whether each gene independently influences human triglyceride concentrations. (doe.gov)
  • However, little information has been gathered to date regarding the genomic location of drought-regulated genes, either expressed throughout plant development or at late reproductive stages influencing seed yield and quality. (biomedcentral.com)
  • Members of the apolipoprotein gene cluster (APOA1/C3/A4/A5) on human chromosome 11q23 play an important role in lipid metabolism. (doe.gov)
  • We also analyzed 17 Y-chromosome STRs in 30 individuals to assess the paternal gene pool. (bioone.org)
  • The Malanis are characterized by a generally low Y-chromosome haplotype diversity. (bioone.org)
  • The VDR gene is located on chromosome 12q12-14, which contains two promoters and 8 exons [ 11 ]. (hindawi.com)
  • Stargardt disease (STGD1) is a form of inherited retinal dystrophy attributed to variants affecting function of the large ABCA4 gene and is arguably the most complex monogenic disease. (nature.com)
  • In order to meet the grand challenge of human genetics, that is, to understand what causes disease and translate this knowledge to improve health outcomes, we need to know the number and population frequency of disease variants, the magnitude of their effects on phenotype and gene-gene and gene-environment interactions. (nature.com)
  • For monogenic disorders, the genetic architecture is simplified as disease variants are, by definition, highly penetrant and environmental and gene-gene interactions are minimized. (nature.com)
  • Patients with ABCA4 -related disease have pathogenic variants in the ABCA4 gene which encodes a large, 2273 amino acid photoreceptor-specific transporter involved in the removal of toxic retinoid compounds from photoreceptors [ 20 ]. (nature.com)
  • Several novel upstream region variants were validated, for instance by their segregation to a single haplotype in heterozygotic subjects. (lu.se)
  • Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been fully characterized. (cancerindex.org)
  • We performed a genome-wide association study (GWAS) and exome-sequencing analysis to identify common and rare genetic variants associated with plasma myeloperoxidase (MPO)-DNA complex levels, a biomarker for NETs, in the population-based Rotterdam Study cohort. (frontiersin.org)
  • We additionally performed exome-sequencing analysis in 960 individuals to investigate rare variants in candidate genes. (frontiersin.org)
  • Genome-wide association studies (GWAS) and exome-sequencing analysis have been successfully implemented as approaches to identify genetic variants associated with disease susceptibility. (frontiersin.org)
  • We performed additional in silico analyses to identify more evidence for the associated variants and genes in relation to the plasma MPO-DNA complex levels. (frontiersin.org)
  • We used logistic regression analysis and Bayesian modeling to identify 2DL2 , 2DL5 , 2DS4-003 , HLA-B-Bw4-Thr , and HLA-B-Bw4-Ile as probably having a significant relationship with disease outcome. (cdc.gov)
  • Conditional logistic regression models did not reproduce the association of HLA-B*07 or the B*07-Cw*07 haplotype with GBM. (cdc.gov)
  • Additionally to long-term processes of gene flow and admixture, the genetic structure of the populations currently inhabiting the area has been impacted by recent events of cultural isolation and local differentiation 20 , 21 . (nature.com)
  • Furthermore, Φ(st)-based genetic distance computation and pair-wise analysis of molecular variance (AMOVA) test were carried out. (nih.gov)
  • To identify the genetic defect in Spanish families with Usher syndrome (USH) and probable involvement of the CLRN1 gene. (molvis.org)
  • Prospective association analysis based on core drought-regulated genes may simplify the process of identifying favourable alleles, and help to understand the genetic basis of the response to terminal drought. (biomedcentral.com)
  • While the productivity of the cereals has risen greatly since their domestication, in response to farmer selection and methodical breeding, there are indications that the increasing fixation of elite alleles in modern breeding germplasm is already inhibiting further genetic gain. (biomedcentral.com)
  • We report haplotyping data for 17 starch biosynthesis/degradation genes demonstrating the broad diversity among H. spontaneum accessions and H. vulgare landraces but rather limited genetic variance in the current elite breeding germplasm by fixing certain haplotypes. (biomedcentral.com)
  • The population structure revealed by multidimensional scaling analysis of standard genetic distances lends support to the AMOVA. (bioone.org)
  • Genetic drift and limited gene flow leading to reduced genetic diversity were important in determining the present genetic structure of the highly endogamous Malana village. (bioone.org)
  • Genetic cluster analysis of the microsatellite markers produced four major clusters, which showed near-perfect correspondence with the four self-reported race/ethnicity categories. (blogspot.com)
  • Clinical application of NGS-based SNP haplotyping for the preimplantation genetic diagnosis of primary open angle glaucoma. (cdc.gov)
  • Genetic epidemiology of glioblastoma multiforme: confirmatory and new findings from analyses of human leukocyte antigen alleles and motifs. (cdc.gov)
  • ABCA4- related retinal dystrophies have a major impact on quality of life and clinical interventions including stem cell therapy, gene replacement therapy, and pharmacological agents are currently being developed [ 21 ]. (nature.com)
  • An analysis of molecular variance (AMOVA) differentiates Malanis from the rest of the comparison populations. (bioone.org)
  • Construction of CYP1B1 gene haplotypes predisposing to primary congenital glaucoma through allele-specific PCR/restriction fragment length polymorphism analysis]. (cdc.gov)
  • The high level of haplotype variation among starch biosynthesis/degradation genes in the progenitors of cultivated barley shows that domestication and breeding have greatly eroded their allelic diversity in current elite cultivars. (biomedcentral.com)
  • This may be due to the loss of intestinal lactase in adulthood, a condition transmitted by an autosomal recessive gene, which differs in humans according to race. (researchgate.net)
  • Susceptibility/resistance of human populations to severe falciparum malaria has been associated with variations in more than 30 genes. (biomedcentral.com)
  • When comparing our population with the Apulia sample previously investigated, the AMOVA analysis detected no evidence for significant differentiation. (nih.gov)
  • The expression patterns of drought regulated genes were monitored during plant ontogeny, mapped and the location of these genes was incorporated into a comprehensive barley SNP linkage map. (biomedcentral.com)
  • Haplotypes and linkage disequilibrium (LD) plots were generated using PHASE and Haploview, respectively. (biomedcentral.com)
  • Upstream sequences were also identified for a set of previously uncharacterized germline gene alleles. (lu.se)
  • Desk S5 unidentified alleles comparison Previously. (findadig.com)
  • Microarray analysis revealed the previously reported mutation p.Y63X in two unrelated patients, one of them homozygous for the mutation. (molvis.org)
  • Nonetheless, HLA-A*32, which has previously been shown to predispose GBM patients to a favorable prognosis, was negatively associated with occurrence of GBM (odds ratio = 0.41, p = 0.04 by univariate analysis). (cdc.gov)
  • A network analysis indicates that two closely related haplotypes account for a large proportion of Malani Y chromosomes. (bioone.org)
  • Upstream and downstream sequences of immunoglobulin genes may affect the expression of such genes. (lu.se)
  • The pipeline handles gene project ambiguities also, which is important in the analysis of data sets of partial sequences specifically. (findadig.com)
  • We discovered that an individual nucleotide polymorphism differentiating between your two noted T cell receptor Beta D2 (TRBD2) alleles is certainly strongly connected with dramatic adjustments in the portrayed repertoire. (findadig.com)
  • Exploratory analysis through classification trees pointed towards a potential association between the Gln27Glu polymorphism and mortality in older individuals. (biomedcentral.com)
  • To investigate the correlation between the polymorphism of estrogen receptor β gene (ESR2) rs3020450 and cancer susceptibility, and explore the epidemiological significance and the effect of ESR2 expression levels on the prognosis of ovarian cancer. (cancerindex.org)
  • Based on meta-analysis the association between ESR2 rs3020450 polymorphism and cancer susceptibility was estimated and a case-control design was used to verify this result in ovarian cancer. (cancerindex.org)
  • The pooled analysis indicated no significant correlation between the ESR2 rs3020450 polymorphism and the cancer susceptibility. (cancerindex.org)
  • Based on meta-analysis and case-control pooled results, ARP and PARP were evaluated respectively in allele (21.95% and7.97%), heterozygote (36.99% and 12.11%) and dominant model (36.84% and 12.97%) of rs3020450 polymorphism in ovarian cancer. (cancerindex.org)
  • Vitamin D receptor (VDR) gene polymorphism is considered to be an important cause of cancer development. (hindawi.com)
  • Results Multiple regression analysis demonstrated that the rs12093097 was the only significant factor that correlated with %ΔIOP (p=0.039). (bmj.com)
  • Among estimated haplotypes, one haplotype that contained the minor allele only in rs3753380, was significantly correlated with low responders even after correction for multiple test (permutation test, p=0.037). (bmj.com)
  • This gene encodes a member of the family of estrogen receptors and superfamily of nuclear receptor transcription factors. (cancerindex.org)
  • The four SNP are located in different regions of the VDR gene and are potentially linked to many diseases [ 11 , 12 ]. (hindawi.com)
  • We report on retinal disease progression in homozygous patients, providing valuable allele-specific insights. (nature.com)
  • A mutation in codon 29 (K56M, rs5491) of the ICAM1 gene was identified in the Kilifi region of Kenya and homozygotes for the mutation were found to be more frequent in patients suffering from cerebral malaria than in controls [ 7 ]. (biomedcentral.com)
  • 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)
  • 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)
  • 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)
  • 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)
  • RIViT-seq technology could speed up associating transcription factors with their target genes. (doe.gov)
  • Search the gene expression profiles from curated DataSets in the Gene Expression Omnibus (GEO) repository. (cancerindex.org)
  • the G allele was a risk factor for malaria in the endemic region, but exhibited significant association with protection from disease in the non-endemic region. (biomedcentral.com)
  • Sequencingbased HLA-A genotyping established that A*3201 was the single A*32 allele underlying the observed association. (cdc.gov)
  • Further analyses restricted to female GBM cases and controls revealed a second association with a specific HLA-B sequence motif corresponding to Bw4-80Ile (odds ratio = 2.71, p = 0.02). (cdc.gov)
  • In a previous study, several HLA-B and HLA-C alleles and haplotypes were positively or negatively associated with the occurrence and prognosis of glioblastoma multiforme (GBM). (cdc.gov)
  • Pathway analysis of the identified genes showed their involvement in cellular development, molecular transport, RNA trafficking, cell-to-cell signaling and interaction, cellular growth and proliferation. (frontiersin.org)
  • Microvariant alleles were found for the DYS458 and DYS385 markers and sequenced. (nih.gov)
  • In the stratified analysis by cancer types, significantly decreased risk was found in ovarian cancer (AG vs GG: OR = 0.73, 95%CI: 0.53-0.97, P = 0.03). (cancerindex.org)
  • In this first GWAS and exome-sequencing analysis of NETs levels, we found several genes that were associated with NETs. (frontiersin.org)
  • Plants have evolved a range of defence and escape mechanisms [ 1 ], and these are typically mediated by multiple rather than by single genes. (biomedcentral.com)
  • The data highlights the significance of variations in the ICAM1 , PECAM1 and CD36 genes in the manifestation of falciparum malaria in India. (biomedcentral.com)
  • Allele and haplotype analysis also did not disclose any significant difference regarding mortality. (biomedcentral.com)
  • Background: Human leukocyte antigen (HLA) class I genes mediate cytotoxic T-lymphocyte responses and natural killer cell function. (cdc.gov)
  • Haplotypes within a set of 17 starch biosynthesis/degradation genes were defined, and a particularly high level of haplotype variation was uncovered in the genes encoding sucrose synthase (types I and II) and starch synthase. (biomedcentral.com)
  • We genotyped KIRs and HLA class I alleles using DNA from uninfected controls, EVD survivors, and persons who died of EVD. (cdc.gov)