Search results for "SNP"
showing 10 items of 366 documents
Genomic structural diversity in local goats: Analysis of copy-number variations
2020
Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell&rsquo
Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors.
2009
In goats, classical genetic studies reported a large number of alleles at the Agouti locus with effects on coat color and pattern distribution. From these early studies, the dominant A(Wt) (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat ASIP gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-rich carboxy-terminal domain of the protein (p.Ala96Gly, p.Cys126Gly, and p.Val1…
Metodes un programmatūra genoma datu analīzei
2017
Maģistra darba tēma “Metodes un programmatūra genoma datu analīzei” Maģistra darbā apkopota informācija par nozīmīgākajām genoma datu analīzes metodēm. Izpētītas praksē biežāk lietotās metodes SNP (single nucleotide polymorphisms) identifikācijai jaunās paaudzes sekvencēšanas (NGS) datos, pieejamā programmatūra, kurā šīs metodes ir implementētas, un veiktas dažādu metožu un programmu darbības salīdzināšana uz simulētām NGS datu kopām. Salīdzinātas programmas genoma datu analīzei - GemSIM, Bowtie2, Samtools, Bfctools, Gatk. Iegūtie rezultāti pārbaudīti ar un salīdzināti ar simulētām datu kopām. Darbā aprakstīta četru genotipēšanas algoritmu darbība: GenoSNP, Illuminus, CRLMM, un GenCall. Tie…
Genetic structure of Tunisian sheep breeds as inferred from genome-wide SNP markers
2020
Abstract Assessing the status of genetic variability of native sheep breeds could provide important clues for research and policy makers to devise better strategies for the conservation and management of genetic resources. In this study, a genetic investigation of Tunisian sheep breeds using a genome-wide scan of approximately 50,000 SNPs was performed. To reconstruct genetic structure and relationships among four sheep breeds, 40 samples belonging to fat-tailed Barbarine, Queue Fine de l’Ouest, Noire de Thibar and D’Man breeds were genotyped using Illumina Ovine SNP50 BeadChip. Tunisian breeds averaged 96 % polymorphic loci with an expected heterozygosity (He = 0.36). Genetic analysis of r…
Rash and multiorgan dysfunction following lamotrigine: could genetic be involved?
2015
We report the case of a 38-year-old woman treated with lamotrigine who experienced multi-organ dysfunction. The patient received the drug at the dose of 100 mg per day. One week later, the treatment was suspended because of an extensive body rash. Twenty-four hours later, the patient appeared drowsy and stuporous and was hospitalized. On the fifth day, the patient was admitted with a clinical picture of acute multi-organ failure in our Institute, where, she, despite the support of vital functions with vasoactive drugs, continuous hemofiltration and ventilation with oxygen, died. Serum lamotrigine concentration was measured 110 h after its last dose and the drug resulted to be still present …
Therapeutic options for homozygous familial hypercholesterolemia: the role of Lomitapide
2020
Background:Lomitapide (Juxtapid® in US and Lojuxta® in Europe) is the first developed inhibitor of the Microsomal Triglyceride Transfer Protein (MTP) approved as a novel drug for the management of Homozygous Familial Hypercholesterolemia (HoFH). It acts by binding directly and selectively to MTP thus decreasing the assembly and secretion of the apo-B containing lipoproteins both in the liver and in the intestine.Aims:The present review aims at summarizing the recent knowledge on lomitapide in the management of HoFH.Results:The efficacy and safety of lomitapide have been evaluated in several trials and it has been shown a reduction of the plasma levels of Low-Density Lipoprotein Cholesterol …
Genome-wide association study identifies five susceptibility loci for follicular lymphoma outside the HLA region.
2014
Genome-wide association studies (GWASs) of follicular lymphoma (FL) have previously identified human leukocyte antigen (HLA) gene variants. To identify additional FL susceptibility loci, we conducted a large-scale two-stage GWAS in 4,523 case subjects and 13,344 control subjects of European ancestry. Five non-HLA loci were associated with FL risk: 11q23.3 (rs4938573, p = 5.79 × 10 -20) near CXCR5; 11q24.3 (rs4937362, p = 6.76 × 10 -11) near ETS1; 3q28 (rs6444305, p = 1.10 × 10 -10) in LPP; 18q21.33 (rs17749561, p = 8.28 × 10 -10) near BCL2; and 8q24.21 (rs13254990, p = 1.06 × 10 -8) near PVT1. In an analysis of the HLA region, we identified four linked HLA-DRß1 multiallelic amino acids at p…
Genome-wide mapping of copy number variations in patients with both anorectal malformations and central nervous system abnormalities
2014
Background: Anorectal malformations (ARM) have a prevalence of around 1 in 2500 live births. In around 50% of patients, the malformation is isolated, while in the remainder it arises within the context of complex genetic abnormalities or a defined genetic syndrome. Recent studies have implicated rare copy number variations (CNVs) in both isolated and nonisolated ARM, and identified plausible candidate genes. Methods: In the present study, array-based molecular karyotyping was performed to identify causative CNVs in 32 sporadic ARM patients with comorbid abnormalities of the central nervous system (CNS). This phenotype was selected to enrich for rare CNVs, since previous research has implica…
A Genome-wide Association Study of Early-onset Breast Cancer Identifies PFKM as a Novel Breast Cancer Gene and Supports a Common Genetic Spectrum for…
2014
Abstract Early-onset breast cancer (EOBC) causes substantial loss of life and productivity, creating a major burden among women worldwide. We analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 population control women ages ≤ 51 years. The SNPs with smallest P values were examined in a replication set of 3,470 EOBC cases and 5,475 control women. We also tested EOBC association with 19,684 genes by annotating each gene with putative functional SNPs, and then combining their P values to obtain a gene-based P value. We examined the gene with smallest P value for replication in 1,145 breast cancer cases and 1,142 control …
Estimation of ordered response models with sample selection
2011
We introduce two new Stata commands for the estimation of an ordered response model with sample selection. The opsel command uses a standard maximum-likelihood approach to fit a parametric specification of the model where errors are assumed to follow a bivariate Gaussian distribution. The snpopsel command uses the semi-nonparametric approach of Gallant and Nychka (1987, Econometrica 55: 363–390) to fit a semiparametric specification of the model where the bivariate density function of the errors is approximated by a Hermite polynomial expansion. The snpopsel command extends the set of Stata routines for semi-nonparametric estimation of discrete response models. Compared to the other semi-n…