Search results for "SNP"
showing 10 items of 366 documents
Genome-wide homozygosity in Maremmana cattle
2017
The current availability of large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of patterns of genetic diversity and of genome-wide homozygosity in animal populations. The aim of this work was to estimate genetic diversity and homozygosity in the Maremmana cattle breed. We used a sample of 149 animals (males and females) geno-typed with the BovineSNP50 v2 (54K) Illumina BeadChip. After editing for call-rate >0.9 and removing SNP unassigned or on the sex chromosomes, 128 animals and 50,814 SNPs were left. We estimated the following genetic parameters: observed and expected heterozygosity (Ho and He), minor …
Postnatal overfeeding in rats leads to moderate overweight and to cardiometabolic and oxidative alterations in adulthood.
2011
In contrast to the masses of data on obesity, few data are available concerning the cardiometabolic and oxidative consequences of moderate overweight. The model of postnatal overfeeding (OF) induces an increase in body weight at weaning that remains during adult life. Litters of Wistar rats were either maintained at 12 pups (normal-fed group, NF), or reduced to 3 pups at birth in order to induce OF. At 6 months of age, metabolic parameters, circulating oxidative stress and aortic and coronary vasoreactivity were assessed. Cardiac susceptibility to ischemia-reperfusion injury was also evaluated ex vivo as were markers of cardiac remodeling. OF led to an increase in body weight at weaning (+5…
Caratterizzazione genetica della razza Bracco Francese ed analisi comparative con le principali razze canine
2018
Il sequenziamento del genoma canino ha contribuito a migliorare l’accuratezza delle stime di diversità genetica ed ha anche generato diversi studi sulle relazioni tra le diverse razze allevate (Vaysse et al., 2011; Parker et al., 2017). Tuttavia, alcune razze rimangono ancora poco caratterizzate. È il caso del Bracco Francese tipo Pyrénées. Lo scopo di questo lavoro è stato quello di caratterizzare a livello genomico la razza e studiarne le relazioni con altre razze allevate nel mondo. Sono stati raccolti i campioni di sangue da 48 individui. La genotipizzazione è stata condotta mediante l’Illumina CanineHD BeadChip (173.662 marcatori). Diversi parametri di diversità genetica sono stati cal…
Variable-order reference-free variant discovery with the Burrows-Wheeler Transform
2020
Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision of previous de Bruijn graphs based tools by overcoming several of their limitations, namely: (i) the need to establish a fixed value, usually small, for the order k, (ii) the loss of important information such as k-mer coverage and adjacency of k-mers within the same read, and (iii) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory con…
Angiogenesis-related prognosis in patients with oral squamous cell carcinoma-role of the VEGF +936 C/T polymorphism.
2014
BACKGROUND: The aim of the study was the immunohistological assessment of VEGF-single nucleotide polymorphism (SNP)-related angiogenic activity in oral squamous cell carcinoma (OSCC) in correlation with prognosis. METHODS: Fifty OSCC samples were immunostained with CD31-antibodies. Mean microvessel density (MVD) and staining intensity were determined and associated with clinicopathological/prognostic features as well as with the VEGF +936C/T SNP. RESULTS: A significant higher MVD could be seen for T3 and T4 compared with T1 and T2, N > 0 vs. N0 as well as G3–G4 vs. G1–G2 OSCCs (all: P < 0.05). A higher MVD was also associated with increased and earlier rates of local relapses, more metastas…
PECAM-1/CD31 in infarction and longevity.
2007
: Inflammation has recently proven to be associated with the pathogenesis of atherosclerosis and inflammatory genes are good candidates for the risk of developing atherosclerosis. The early phase of atherosclerosis involves the recruitment of inflammatory cells from the circulation and their transendothelial migration. This process is mainly mediated by cellular adhesion molecules, which are expressed by the vascular endothelium and by circulating leukocytes in response to several inflammatory stimuli. Adhesion of circulating cells to the arterial surface is among the first detectable events in atherogenesis. Cellular adhesion molecules, expressed by the vascular endothelium and by circulat…
CD36 AA genotype is associated with decreased lipid taste perception in young obese, but not lean, children.
2015
Obesity is an alarming threat for all age groups, including children. Fat overconsumption is one of the factors that directly influences this pathology. Recent studies have suggested that a common variant in the CD36 gene, that is, single-nucleotide polymorphism (SNP) rs1761667-A allele, that reduces CD36 expression, associates with high oral fat detection thresholds in some obese subjects. The objective was to assess fatty acid sensitivity in relation to CD36 SNP in young lean and obese children. We studied lingual detection thresholds for emulsions, containing oleic acid, in Algerian children (n=116, age=8±0.5 years) who were divided into two groups: obese (n=57; body mass index (BMI) z-s…
Breast cancer genome-wide association studies: there is strength in numbers.
2012
Breast cancer (BC) is a heterogeneous disease that exhibits familial aggregation. Family linkage studies have identified high-penetrance genes, BRCA1, BRCA2, PTEN and TP53, that are responsible for inherited BC syndromes. Moreover, a combination of family-based and population-based approaches indicated that genes involved in DNA repair, such as CHEK2, ATM, BRIP and PALB2, are associated with moderate risk. Therefore, all of these known genes account for only 25% of the familial aggregation cases. Recently, genome wide association studies (GWAS) in BC revealed single nucleotide polymorphisms (SNPs) in five novel genes associated to susceptibility: TNRC9, FGFR2, MAP3K1, H19 and lymphocyte-spe…
Identification of Risk Loci for Radiotoxicity in Prostate Cancer by Comprehensive Genotyping of
2021
Simple Summary Genetic variability in transforming growth factor beta pathway (TGFB) has been reported to affect adverse events in radiotherapy. We investigated 40 germline polymorphisms in peripheral blood cells, covering the entire common genetic variability in the TGFβ1 ligand (gene TGFB1) and the TGFβ receptor-1 (TGFBR1) in 240 patients treated with primary radiotherapy for prostate cancer. Human lymphoblastoid cell lines (LCLs) were used to assess whether TGFB1 and TGFBR1 polymorphisms impact DNA repair capacity following single irradiation with 3 Gy. Upon adjustment for multiplicity testing, for one polymorphism (rs10512263 in TGFBR1, C-variant allele, n = 35), a statistically signifi…
Genome-Wide Haplotype Analysis of Cis Expression Quantitative Trait Loci in Monocytes
2013
In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL) was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. 19,805 RNA probes were assessed for cis haplotypic regulation through investigation of ∼2,1×109 haplotypic combinations. 2,650 probes demonstrated haplotypic p-values >104-fold smaller than the best single SNP p-value. Replication of significant haplotype effects were tested f…