Search results for "single-nucleotide polymorphism"

Education modulates the association of the FTO rs9939609 polymorphism with body mass index and obesity risk in the Mediterranean population

2012

Objective To define whether the rs9939609 FTO (fat mass and obesity associated) single nucleotide polymorphism (SNP) is associated with anthropometric measurements and its modulation by educational level in a Mediterranean population. Methods We studied 3 independent adult samples: a random sample (n = 1580) from the general population (GP), obese hospital patients (OHP) (n = 203) and elderly subjects (n = 1027) with high cardiovascular risk (HCR). Weight and height were directly measured. Education and physical activity (PA) were measured using questionnaires. Results The rs9939609 presented heterogeneous associations with BMI. In the GP, the minor A-allele was significantly associated wit…

Rapid microarray-based typing of forensic SNPs

2006

The single base extension-tag array (SBE-Tag Array) method is carried out on glass slides and combines the specificity of minisequencing for SNP typing with the high throughput capacity of microarrays. Following multiplex PCR, a single tube SBE reaction is carried out, and the fluorescent labelled extension products are hybridized to the complementary DNA sequence tag (cTag) immobilized on a glass slide for locus-specific laser scan analysis. The aim is to prove and optimise the conventional microarray reaction on accuracy and efficiency for forensic applications. © 2005 Elsevier B.V. All rights reserved.

Analyzing Illumina Gene Expression Microarray Data from Different Tissues: Methodological Aspects of Data Analysis in the MetaXpress Consortium

2012

Microarray profiling of gene expression is widely applied in molecular biology and functional genomics. Experimental and technical variations make meta-analysis of different studies challenging. In a total of 3358 samples, all from German population-based cohorts, we investigated the effect of data preprocessing and the variability due to sample processing in whole blood cell and blood monocyte gene expression data, measured on the Illumina HumanHT-12 v3 BeadChip array. Gene expression signal intensities were similar after applying the log(2) or the variance-stabilizing transformation. In all cohorts, the first principal component (PC) explained more than 95% of the total variation. Technic…

Polymorphisms within the TNFSF4 and mapkapk2 loci influence the risk of developing invasive aspergillosis: A two-stage case control study in the cont…

2020

Here, we assessed whether 36 single nucleotide polymorphisms (SNPs) within the TNFSF4 and MAPKAPK2 loci influence the risk of developing invasive aspergillosis (IA). We conducted a twostage case control study including 911 high-risk patients diagnosed with hematological malignancies that were ascertained through the aspBIOmics consortium. The meta-analysis of the discovery and replication populations revealed that carriers of the TNFSF4rs7526628T/T genotype had a significantly increased risk of developing IA (p = 0.00022). We also found that carriers of the TNFSF4rs7526628T allele showed decreased serum levels of TNFSF14 protein (p = 0.0027), and that their macrophages had a decreased fungi…

Identifying four Trypanosoma cruzi I isolate haplotypes from different geographic regions in Colombia

2007

Abstract Trypanosoma cruzi has been classified into the groups T. cruzi I and T. cruzi II. The latter is subdivided into five smaller lineages based on multilocus enzyme electrophoresis and random amplified polymorphic DNA, designated as IIa-IIe, which shows correspondence with rRNA/mini-exon lineages. Twelve previously characterised T. cruzi isolates from different hosts, including humans, Didelphis marsupialis, and triatomines were analysed to establish genetic variability in T. cruzi group T. cruzi I isolates from different geographical regions of Colombia. DNA samples were sequenced based on the mini-exon gene intergenic region. Sequences were analysed using Clustal W, Staden 1.5 and ME…

Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance sur…

2020

9 páginas, 3 figuras

Study of polymorphisms in the promoter region of ovine β-lactoglobulin gene and phylogenetic analysis among the Valle del Belice breed and other shee…

2012

The aim of this work was to sequence the promoter region of b-lactoglobulin (BLG) gene in four sheep breeds, in order to identify polymorphisms, infer and analyze haplotypes, and phylogenetic relationship among the Valle del Belice breed and the other three breeds considered as ancestors. Sequencing analysis and alignment of the obtained sequences showed the presence of 36 single nucleotide polymorphisms (SNPs) and one deletion. A total of 22 haplotypes found in ‘‘best’’ reconstruction were inferred considering the 37 polymorphic sites identified. Haplotypes were used for the reconstruction of a phylogenetic tree using the Neighbor-Joining algorithm. The number of polymorphisms identified s…

Single nucleotide polymorphisms of the vascular endothelial growth factor gene associated with incidence of oral squamous cell carcinoma

2010

J Oral Pathol Med (2010) 39: 786–792 Background:  Vascular endothelial growth factor (VEGF) plays an important role in promoting angiogenesis and is overexpressed in several malignancies. Polymorphisms of the VEGF gene can alter VEGF protein expression, which may be biologically significant and account for heterogeneity in disease risk and outcome. The aim of this case–control study was to evaluate potential associations between single nucleotide polymorphisms (SNP) of the VEGF gene with susceptibility of oral squamous cell carcinoma (OSCC). Patients and methods:  Five VEGF SNP (−1154 G/A, +405 G/C, +936 C/T, −2578 C/A and −460 C/T) were determined in peripheral blood isolated from 80 patie…

2015

AbstractPrimary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10−8) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine–cytokine pathways, for which relevant therapies exist.

IL12A, MPHOSPH9/CDK2AP1 and RGS1 are novel multiple sclerosis susceptibility loci

2010

A recent meta-analysis identified seven single-nucleotide polymorphisms (SNPs) with suggestive evidence of association with multiple sclerosis (MS). We report an analysis of these polymorphisms in a replication study that includes 8,085 cases and 7,777 controls. A meta-analysis across the replication collections and a joint analysis with the discovery data set were performed. The possible functional consequences of the validated susceptibility loci were explored using RNA expression data. For all of the tested SNPs, the effect observed in the replication phase involved the same allele and the same direction of effect observed in the discovery phase. Three loci exceeded genome-wide significa…