Search results for "snps"
showing 10 items of 74 documents
On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
2020
Background In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of commo…
Genetic risk profiles for Alzheimer's disease: Integration of APOE genotype and variants that up-regulate inflammation
2007
BACKGROUND: A number of studies associate Alzheimer's disease with APOE polymorphism and alleles which favor the increased expression of immunological mediators such as cytokines or acute phase proteins. We integrated this information to better define risk and determine the relative importance of APOE and immunological mediators. METHODS: We investigated functional gene variants for APOE, IL-10 (3 loci), ACT (2 loci), HMGCR, IL-1alpha, IL-1beta, TNF-alpha, IFN-gamma, and IL-6 found for 260 AD patients and 190 controls enrolled in Northern Italy. A fuzzy latent classification approach, namely grade-of-membership analysis (GoM), was taken to identify extreme pure type risk sets, or profiles. …
Selection signatures of fat tail in sheep
2017
The investigation of the genes with a role in lipid metabolism enjoy considerable scientific and commercial interest because of the strong correlations between fat deposition and the risk of cardiovascular disease. The fat tail characteristic of sheep is the adaptive response to harsh environment, and beyond representing a valuable energy reserve for facing future climate changes provides clues for elucidating the physiology of fat deposition. Studies on various sheep populations detected fat-tail signatures on chromosomes 2, 3, 5, 6, 7 and 13. Fat-tailed sheep represent about 25% of the world’s sheep population, and the genes with a role in this phenotype are likely not the same for every …
Low sensitivity of the MPT64 identification test to detect lineage 5 of the Mycobacterium tuberculosis complex
2018
Abstract: Purpose. Differentiation of the Mycobacterium tuberculosis complex (MTBc) from non-tuberculous mycobacteria (NTM) is important for tuberculosis diagnosis and is a prerequisite for reliable phenotypic drug-resistance testing. We evaluated the performance of the rapid MPT64 antigen identification test for the detection of Mycobacterium africanum lineage 5 (MAF L5). Methodology. Smear-positive tuberculosis patients' sputa were included prospectively. Culture was performed on Lowenstein-Jensen medium and, when positive, the MPT64 test and the classical para-nitro benzoic acid susceptibility and heat-labile catalase (PNB/catalase) identification tests were performed. The MPT64 test was…
Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems
2021
Abstract Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italia…
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…
Tracking Zebu Introgression in Mediterranean Cattle Breeds
2017
A recent work investigating genetic origin, admixture and population history of primitive European cattle highlighted, by using genome-wide single nucleotide polymorphisms, zebu gene flow in the Balkan and Italian Podolic cattle populations. Haemoglobin protein polymorphism analysis in Italian breeds highlighted the presence of zebuine markers in both Italian Podolic and Alpine Grey cattle. Based on the above evidences, we here specifically look for genomic regions of zebuine ancestry in a different dataset of 50K genotypes from Mediterranean breeds including 29 Marismena (Spain); 30 Bazadaise and 30 Gasconne (France); 24 Alpine Grey, 97 Piemontese, 51 Chianina, 5 Marchigiana, 121 Romagnola…
Polymorphisms of β-defensin genes in Valle del Belice dairy sheep
2011
The aim of this work was to study β-defensin 1 (SBD1) and β-defensin 2 (SBD2) genes in Valle del Belice dairy sheep in order to identify polymorphisms that can be utilized as markers of the analyzed genes, and search for the functional effects and roles of the identified polymorphisms (variation of the amino acid sequence of the protein and stability of mRNA molecule). The study was conducted on 300 randomly selected animals belonging to four flocks. A total of seven SNPs were identified, two in SBD1 and five in SBD2. The two SNPs identified in SBD2 coding region, at position 1659 and position 1667, were non-synonymous, leading to amino acid changes in the protein product. Nevertheless, the…
Interleukin-10 and interleukin-18 promoter polymorphisms in an Italian cohort of patients with undifferentiated carcinoma of nasopharyngeal type.
2004
Purpose: Cytokines such as IL-10 and IL-18 seem to be involved in the inflammatory response of undifferentiated carcinoma of nasopharyngeal type (UCNT). The aim of this study was to evaluate the correlation between functional single nucleotide polymorphisms (SNPs) in the promoter region of IL-10 and IL-18 genes and the virological and clinical characteristics in a large case series of Caucasian patients suffering from UCNT, a tumor regularly associated with the Epstein Barr Virus (EBV). Methods: Eighty-nine patients with histologically confirmed UCNT and 130 healthy donors were included in our study. DNA was examined for the polymorphisms of IL-10 gene at positions –1082, −819, −592 by dire…
Genomic characterization of Algerian Guelmoise cattle and their genetic relationship with other North African populations inferred from SNP genotypin…
2018
International audience; Understanding between and within-breeds genetic variability is essential in the choice of conservation management decisions for threatened populations. In this study we assessed the genetic diversity of the Algerian Guelmoise cattle (GUE) by analyzing data on 24 GUE individuals genotyped for the Illumina BovineSNP50 BeadChipv2. We also provided a detailed description of the population structure of GUE using comparisons with 23 worldwide cattle populations, selected as being representative of African, South European and indicine populations, in addition to four North African populations. We show that GUE is an admixed population which has strong genetic similarity to …