Search results for "snps"
showing 10 items of 74 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 …
Haplotypes of Single Nucleotide Polymorphisms (SNPs) in casein loci of Girgentana goats explain isoelectrofocusing results.
2006
Goat milk, cheese and yoghurt offer an alternative to cow milk products. In Sicily one of the important goat breeds reared is the Girgentana. Traditionally the milk from Girgentana goats was used for nourishment of infants and elderly. Recently, the Girgentana breed has been in decline. This of concern, as the Girgentana may carry unique milk protein genetic variants. If health benefits of Girgentana goat milk is proven, then increasing production from this population will be of great interest. The most abundant proteins in goat milk, as in other milks, are the caseins, αS1-, β-, αS2- and κ-casein, coded by the loci CSN1S1, CSN2, CSN1S2 and CSN3 respectively. In other goat breeds, the casei…
CLINICAL, BIOMOLECULAR AND IMMUNOLOGICAL INVESTIGATION OF KNEE OSTEOARTHRITIS
2014
Introduction. Osteoarthritis (OA) is a slowly progressive disorder characterized by a gradual loss of articular cartilage. The OA classification is mainly based on clinical and radiographic evaluations, using the Knee Society Score (AKSS) and the Kellgren and Lawrence (KL) scale. Single nucleotide polymorphisms (SNPs) in frzb, matn3,aspn, pthr2, gdf5 and dvwa genes are involved in OA susceptibility. However, very few studies in Caucasian people describe the association between KL grading scale and genetical alterations. In this study we assessed the associations between KL grade, clinical features,SNPs and inflammatory mediators in Sicilian individuals Methods. We enrolled 66 patients with …
Caratterizzazione genomica delle razze bovine autoctone italiane
2018
Negli ultimi cinquant'anni, a causa della sostituzione con le razze cosmopolite, le razze zootecniche locali hanno subito una forte contrazione numerica. Tuttavia, esse rappresentano un’importante patrimonio, in grado, tra le altre cose, di valorizzare ambienti marginali. Sono spesso legate anche a produzioni tipiche di alta qualità. La loro caratterizzazione rappresenta un passo essenziale verso eventuali piani di recupero, conservazione e valorizzazione. Il presente studio è stato condotto al fine di caratterizzare a livello genomico le razze bovine locali allevate in Italia. Sono stati campionati un totale di 814 animali appartenenti a 30 razze italiane e a 2 razze cosmopolite (Charolais…
THE EFFECT OF CYP3A5 AND ABCB1 SINGLE NUCLEOTIDE POLYMORPHISMS ON TACROLIMUS DOSE REQUIREMENTS IN CAUCASIAN LIVER TRANSPLANT PATIENTS
2008
Identificazione di una nuova variante alla κ-caseina nella razza caprina Girgentana
2013
La κ-caseina è la lattoproteina che determina la grandezza e la funzione specifica delle micelle nel latte e la sua idrolisi, chimosina dipendente, è responsabile della coagulazione del latte stesso. Il gene della κ-caseina comprende 5 esoni. Ad oggi sono state identificate 16 varianti alleliche, di cui 13 sono varianti proteiche e 3 mutazioni silenti, per un totale di 15 siti polimorfici.Lo scopo di questo lavoro è stato la caratterizzazione dell’esone 4 del gene della κ-caseina nella razza caprina Girgentana. Un nuova variante alleliche, denominata X, è stata riscontrata con una frequenza relativamente bassa (0,04).
Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior
2010
Contains fulltext : 89305.pdf (Publisher’s version ) (Closed access) Smoking is a common risk factor for many diseases. We conducted genome-wide association meta-analyses for the number of cigarettes smoked per day (CPD) in smokers (n = 31,266) and smoking initiation (n = 46,481) using samples from the ENGAGE Consortium. In a second stage, we tested selected SNPs with in silico replication in the Tobacco and Genetics (TAG) and Glaxo Smith Kline (Ox-GSK) consortia cohorts (n = 45,691 smokers) and assessed some of those in a third sample of European ancestry (n = 9,040). Variants in three genomic regions associated with CPD (P < 5 x 10(-8)), including previously identified SNPs at 15q25 repre…
Detecting mutations by eBWT
2018
In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts how many copies of any nucleotide are expected inside each such cluster, and how an elegant and precise LCP array based procedure can locate these clusters in the eBWT. Our findings are very general and can be applied to a wide range of different problems. In this paper, we consider the case of alignment-free and reference-free SNPs discovery in multiple collections of reads. We note that, in accordance with our theoretical results, SNPs are clustered in th…
Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.).
2015
How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35‰ in the North Sea to 7‰ within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the …
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations
2013
Elevated serum urate concentrations can cause gout, a prevalent and painful inflammatory arthritis. By combining data from >140,000 individuals of European ancestry within the Global Urate Genetics Consortium (GUGC), we identified and replicated 28 genome-wide significant loci in association with serum urate concentrations (18 new regions in or near TRIM46, INHBB, SFMBT1, TMEM171, VEGFA, BAZ1B, PRKAG2, STC1, HNF4G, A1CF, ATXN2, UBE2Q2, IGF1R, NFAT5, MAF, HLF, ACVR1B-ACVRL1 and B3GNT4). Associations for many of the loci were of similar magnitude in individuals of non-European ancestry. We further characterized these loci for associations with gout, transcript expression and the fractional…