Search results for "Single nucleotide polymorphism"

showing 10 items of 69 documents

Pharmacogenetic considerations for optimizing tacrolimus dosing in liver and kidney transplant patients

2013

The introduction of tacrolimus in clinical practice has improved patient survival after organ transplant. However, despite the long use of tacrolimus in clinical practice, the best way to use this agent is still a matter of intense debate. The start of the genomic era has generated new research areas, such as pharmacogenetics, which studies the variability of drug response in relation to the genetic factors involved in the processes responsible for the pharmacokinetics and/or the action mechanism of a drug in the body. This variability seems to be correlated with the presence of genetic polymorphisms. Genotyping is an attractive option especially for the initiation of the dosing of tacrolim…

Graft Rejectionmedicine.medical_specialtyCYP3A5ATP Binding Cassette Transporter Subfamily BCYP3A4Genotypemedicine.medical_treatmentPharmacologyLiver transplantationBioinformaticsOrgan transplantationTacrolimusCalcineurin inhibitorMedicineCytochrome P-450 CYP3AHumansDrug Dosage CalculationsDosingATP Binding Cassette Transporter Subfamily B Member 1Topic HighlightKidney transplantLiver transplantKidney transplantationBiotransformationPolymorphism Geneticbusiness.industryPharmacogeneticGraft SurvivalGastroenterologyABCB1General Medicinemedicine.diseaseKidney TransplantationTacrolimusLiver TransplantationSingle nucleotide polymorphismTransplantationsurgical procedures operativePhenotypeTreatment OutcomePharmacogeneticsTacrolimuSettore BIO/14 - FarmacologiaPersonalized medicinebusinessPharmacogeneticsImmunosuppressive Agents

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Comparing RADseq and microsatellites for estimating genetic diversity and relatedness : Implications for brown trout conservation

2019

The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic di…

HETEROZYGOSITY-FITNESS CORRELATIONSSINGLE NUCLEOTIDE POLYMORPHISMCROSS-SPECIES AMPLIFICATIONINBREEDING DEPRESSIONrelatednessLINKAGE DISEQUILIBRIUMDNA-analyysiddRADseqEFFECTIVE POPULATION-SIZER-PACKAGEpopulation geneticsgeneettinen monimuotoisuuskalanviljelytaimenHABITAT FRAGMENTATIONpopulaatiogenetiikkaATLANTIC SALMONfisheriessalmonids1181 Ecology evolutionary biologySALMON SALMO-SALAR

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European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci

2022

A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent seco…

LDQTLPhysiologySLCFruit morphologyMicrobiologiaPlant SciencePortes-lès-ValenceSLLquantitative trait locusSolanum lycopersicumsingle nucleotide polymorphismCrop evolution; diversification; fruit morphology; genome-wide association study; genotyping by sequencing; selection; single nucleotide polymorphismGWASLSLSolanum pimpinellifolium HM ClauseCrop evolutionFarmersSPSolanum lycopersicum var. cerasiformeTomàquets--Conreuminimum allele frequencyMAFPhenotypeDiversificationGenotyping by sequencinglong shelf-lifeGenome-wide association studydiversificationSNPselectionprincipal coordinate analysesGBSFrance Crop evolutionPolymorphism Single Nucleotidegenotyping by sequencingLife ScienceHumansPCoA:Enginyeria agroalimentària::Agricultura::Producció vegetal [Àrees temàtiques de la UPC]SelectionAllelesfruit morphologyGenetic VariationEcologia[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breedingPlant BreedingSolanum lycopersicum L. var. lycopersicumlinkage disequilibriumTomatoes--VarietiesGenome-Wide Association StudyJ Exp Bot

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Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study

2012

BACKGROUND: High plasma HDL cholesterol is associated with reduced risk of myocardial infarction, but whether this association is causal is unclear. Exploiting the fact that genotypes are randomly assigned at meiosis, are independent of non-genetic confounding, and are unmodified by disease processes, mendelian randomisation can be used to test the hypothesis that the association of a plasma biomarker with disease is causal. METHODS: We performed two mendelian randomisation analyses. First, we used as an instrument a single nucleotide polymorphism (SNP) in the endothelial lipase gene (LIPG Asn396Ser) and tested this SNP in 20 studies (20,913 myocardial infarction cases, 95,407 controls). Se…

LOCIMyocardial Infarction030204 cardiovascular system & hematologychemistry.chemical_compound0302 clinical medicineHigh-density lipoproteinGene Frequencyplasma HDL cholesterol ; mendelian randomisation ; MIHDL cholesterolsingle nucleotide polymorphismRisk FactorsGENETIC-VARIANTSARTERY-DISEASEProspective StudiesMyocardial infarction0303 health sciencesHDL cholesterol; myocardial infarction; single nucleotide polymorphismISCHEMIC CARDIOVASCULAR-DISEASEGeneral Medicine3. Good healthCardiologylipids (amino acids peptides and proteins)medicine.medical_specialtyDalcetrapibSingle-nucleotide polymorphismPolymorphism Single Nucleotide03 medical and health sciencesInternal medicinemedicineHumansCORONARY-HEART-DISEASEGenetic Predisposition to DiseaseMETAANALYSIS030304 developmental biologyBLOOD CHOLESTEROLbusiness.industryCholesterolCholesterol HDLCase-control studyCholesterol LDLLipaseOdds ratioMendelian Randomization Analysismedicine.diseaseENDOTHELIAL LIPASEATHEROSCLEROSISchemistryCase-Control StudiesbusinessHIGH-DENSITY-LIPOPROTEINBiomarkersEvacetrapibThe Lancet

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International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways

2015

Primary 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.

Liver CirrhosisGenetics and Molecular Biology (all)pathogenesirisk assessment EMTREE medical terms: Articlegenetic associationgenotypeEMTREE drug terms: chemokine receptor CCR6genetic riskBiochemistrymeta-analysiprimary biliary cirrhosichemokine receptor CCR6 [EMTREE drug terms]single nucleotide polymorphismgenetic variabilityArticle [risk assessment EMTREE medical terms]Liver Cirrhosis BiliarypathogenesisBiliaryChemistry (all)STAT protein GEOBASE Subject Index: disease treatmentcohort analysisgenome wide meta analysis PBCsignal transductiongene locuscohort analysiCBPArticle*Physics and Astronomy (all)macrophage inflammatory protein 3alphaHumanscontrolled studyhumaninterleukin 27genomeBiochemistry Genetics and Molecular Biology (all)meta analysiinterleukin 12p40EMTREE drug terms: chemokine receptor CCR6; interleukin 12; interleukin 12p40; interleukin 27; Janus kinase; macrophage inflammatory protein 3alpha; STAT protein GEOBASE Subject Index: disease treatment; genome; meta-analysis; pathogen; risk assessment EMTREE medical terms: Article; cohort analysis; controlled study; gene locus; genetic association; genetic predisposition; genetic risk; genetic variability; genotype; human; major clinical study; meta analysis; pathogenesis; primary biliary cirrhosis; signal transduction; single nucleotide polymorphismmajor clinical studyprimary biliary cirrhosismeta-analysisdisease treatment [STAT protein GEOBASE Subject Index]Biochemistry Genetics and Molecular Biology (all); Chemistry (all); Physics and Astronomy (all)Humans; Liver Cirrhosis; Biliary; Genome-Wide Association Study; Biochemistry; Genetics and Molecular Biology (all); Chemistry (all); Physics and Astronomy (all)gene locuinterleukin 12genetic predispositionJanus kinasepathogenmeta analysisHumans; Liver Cirrhosis Biliary; Genome-Wide Association Study; Biochemistry Genetics and Molecular Biology (all); Chemistry (all); Physics and Astronomy (all)Genome-Wide Association Study

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Genetic association of interleukin-6 polymorphism (-174 G/C) with chronic liver diseases and hepatocellular carcinoma

2012

Interleukin-6 (IL-6) is a pleiotropic cytokine which is expressed in many inflammatory cells in response to different types of stimuli, regulating a number of biological processes. The IL-6 gene is polymorphic in both the 5’ and 3’ flanking regions and more than 150 single nucleotide polymorphisms have been identified so far. Genetic polymorphisms of IL-6 may affect the outcomes of several diseases, where the presence of high levels of circulating IL-6 have been correlated to the stage and/or the progression of the disease itself. The -174 G/C polymorphism is a frequent polymorphism, that is located in the upstream regulatory region of the IL-6 gene and affects IL-6 production. However, the…

Liver Cirrhosismedicine.medical_specialtyCarcinoma HepatocellularHepatitis C virusSingle-nucleotide polymorphismBiologyChronic liver diseasemedicine.disease_causePolymorphism Single NucleotideGastroenterologyHepatitis B ChronicNon-alcoholic Fatty Liver DiseaseRisk FactorsChronic hepatitis Hepatocellular carcinoma Interleukin-6 Liver cirrhosis Single nucleotide polymorphismsInternal medicineGenotypemedicineHumansGenetic Predisposition to DiseaseTopic HighlightLiver Diseases AlcoholicInterleukin-6Liver NeoplasmsFatty liverGastroenterologyGeneral MedicineHepatitis C ChronicHepatitis Bmedicine.diseaseFatty LiverHepatitis AutoimmunePhenotypeHepatocellular carcinomaImmunologySteatohepatitisWorld Journal of Gastroenterology

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Imbalance between genomic gain and loss identifies high-risk neuroblastoma patients with worse outcomes

2021

Survival in high-risk neuroblastoma (HR-NB) patients remains poor despite multimodal treatment. We aimed to identify HR-NB patients with worse outcomes by analyzing the genomic instability derived from segmental chromosomal aberrations. We calculated 3 genomic instability indexes for primary tumor SNP array profiles from 127 HR-NB patients: (1) Copy number aberration burden (%gainslength+%losseslength), (2) copy number load (CNL) (%gainslength-%losseslength) and (3) net genomic load (NGL) (%gainsamount-%lossesamount). Tumors were classified according to positive or negative CNL and NGL genomic subtypes. The impact of the genomic instability indexes on overall survival (OS) was assessed with…

Male0301 basic medicineGenome instabilityOncologyCancer ResearchCopy number loadSNPa single nucleotide polymorphism arrayNeuroblastoma0302 clinical medicineHigh risk neuroblastomaSegmental chromosomal aberrationsHR high-riskCNA copy number aberrationTumor biologyCNL copy number loaddNGL decreased net genomic loadlcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogensPrognosisPrimary tumornCNL negative copy number loadGI genomic instabilityHomogeneous030220 oncology & carcinogenesisMNA MYCN-amplificationFemaleHR-NB high-risk neuroblastomaNB neuroblastomaSNP arrayOriginal articlemedicine.medical_specialtyDNA Copy Number VariationsiNGL increased net genomic loadpCNL positive copy number loadhetMNA heterogeneous MYCN-amplificationlcsh:RC254-282Polymorphism Single NucleotideGenomic InstabilityUHR ultra-high-riskOS overall survivalNet genomic load03 medical and health sciencesSCA segmental chromosomal aberrationInternal medicineNeuroblastomamedicineHumansNGL net genomic loadGenetic Predisposition to DiseaseGenomic imbalanceGenetic Association StudiesEFS event-free survivalProportional Hazards ModelsChromosome AberrationsPloidieshomMNA homogeneous MYCN-amplificationProportional hazards modelbusiness.industryGene AmplificationGenetic Variationmedicine.diseasePatient Outcome AssessmentCopy number aberration burden030104 developmental biologybusinessNeoplasia

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SARS CoV2 infection _The longevity study perspectives

2021

Graphical abstract

MaleAgingssRNA single-stranded RNARFLP restriction fragment length polymorphismHSPs heat shock proteinsReviewPTMs post-translational modificationsSevere Acute Respiratory SyndromeBiochemistryHIV-1 human immunodeficiency virus-1TNF-α tumor necrosis factor-αEC endothelial cells0302 clinical medicineFluAV influenza A virusI insertionMedicineIFN-γ interferon-γDIC disseminated intravascular coagulationPCR Polymerase Chain Reactionmedia_commonAged 80 and overLongevityRBD receptor-binding domainNeurologyLongevity modelMI myocardial infarctionNK natural killerhPIV2 human parainfluenza virus type 2media_common.quotation_subjectResearching genetic basis of resistance and potential pharmacological targetsLongevityDBP diastolic blood pressureNF-Kb nuclear transcription factor kBRANTES regulated upon activation normal T cell expressed and secretedMphi human macrophages03 medical and health sciencesCox 2 cyclooxygenase 2ORF open reading framePT prothrombin timeSettore MED/05 - Patologia ClinicaHumansMolecular BiologyInflammatory genesARDS acute respiratory distress syndromeNO nitric oxideD deletionCpGIs CpG islandsT2DM type 2 diabetes mellitusmedicine.diseaseFDP fibrin degradation products030104 developmental biologySARS CoV2 severe acute respiratory syndrome Coronavirus 2 virusImmunologyBMI body max indexItalian nonagenarians/centenariansRSV respiratory syncytial virusComplication030217 neurology & neurosurgeryMAPK mitogen-activated protein kinaseIP-10 IFN-γ -Inducible Protein 1040301 basic medicineAT1R activity of angiotensin 1 receptorsDCs dentritic cellsSSCP single strand conformation polymorphismACE/DD polymorphism of the angiotensin converting enzymeFGF21 fibroblast growth factor 21TLR4 toll-like receptor 4NAD nicotinamide adenine dinucleotideACE angiotensin-I converting enzymeAT2R activity of angiotensin 2 receptorsCOVID-19 Coronavirus disease 2019Respiratory distressACE2 angiotensin converting enzyme 2MKP-1 mitogen-activated protein kinase phosphatase-1 ()PD protease domainSNP single nucleotide polymorphismEH essential hypertensionTNFR tumor necrosis factor receptorINR international normalized ratio of the prothrombin timePAI-1 plasminogen activator inhibitor-1Ang angiotensinLPS lipopolysaccharideMCP1 monocyte chemoattractant protein-1medicine.symptomaPTT partial thromboplastin timeBiotechnologyDUSP1 dual specificity phosphatase 1Coronavirus disease 2019 (COVID-19)PC prostate cancerRAS renin-angiotensin aldosterone systemCCR5Δ32 genetic variant of chemokine receptorCOVID-19 Researching genetic basis of resistance and potential pharmacological targets Italian nonagenarians/centenarians Longevity modelAsymptomaticSARS-1 severe acute respiratory syndrome virus 1SIRT-1 Sirtuin 1Th1 t-helper lymphocyte type 1Immune systemROS reactive oxygen speciesTGF-β transforming growth factor betaET-1 endothelin-1ComputingMethodologies_COMPUTERGRAPHICSADAM-17 metallopeptidase domain 17business.industrySARS-CoV-2SBP systolic blood pressureCOVID-19HDACs histone deacetylasesComorbidityImmune Systembusiness5-LO lipoxygenase 5Ageing Research Reviews

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TNF-alpha gene promoter polymorphisms and risk of venous thromboembolism in gastrointestinal cancer patients undergoing chemotherapy

2013

Abstract Background TNF-α has been proposed as a predictive factor for venous thromboembolism (VTE). Genetic polymorphisms could regulate TNF-α production. However, the relationship between TNFA gene variants and VTE is not clarified. This study aims to investigate the predictive role of five different TNFA gene promoter SNPs, or their haplotype combination(s), for a first VTE episode in gastrointestinal cancer out-patients treated with chemotherapy. Patients and methods Serum TNF-α levels and TNFA -863C/A, -857C/T, -376G/A, -308G/A and -238G/A gene promoter polymorphisms were retrospectively evaluated in 314 subjects, including 157 controls and 157 Caucasian patients with histologically di…

MaleAntimetabolitesSettore MED/06 - Oncologia Medicamedicine.medical_treatmentchemotherapyGastroenterologysingle nucleotide polymorphismschemotherapy; gastrointestinal cancer; single nucleotide polymorphisms; tumour necrosis factor-α; venous thromboembolismsingle nucleotide polymorphismPhytogenic80 and overtumour necrosis factor-αPromoter Regions GeneticGastrointestinal NeoplasmsAged 80 and overHazard ratioSingle NucleotideHematologyMiddle AgedAntineoplasticChemotherapy regimenOncologyFemaleFluorouracilmedicine.drugAdultRiskAntimetabolites Antineoplasticmedicine.medical_specialtygastrointestinal cancervenous thromboembolismAntineoplastic AgentsSingle-nucleotide polymorphismIrinotecanPolymorphism Single NucleotidePromoter RegionsGeneticInternal medicinemedicineHumansGenetic Predisposition to DiseaseGastrointestinal cancercardiovascular diseasesPolymorphismRetrospective StudiesAgedChemotherapyTumor Necrosis Factor-alphabusiness.industryHaplotypeOdds ratiomedicine.diseaseAntineoplastic Agents PhytogenicIrinotecanHaplotypesCase-Control StudiesImmunologyCamptothecinHuman medicinePolymorphism Single Nucleotide; Antimetabolites Antineoplastic; single nucleotide polymorphisms; Humans; Retrospective Studies; Aged; Promoter Regions Genetic; Haplotypes; Aged 80 and over; Adult; gastrointestinal cancer; Genetic Predisposition to Disease; Male; tumour necrosis factor-α; Tumor Necrosis Factor-alpha; Venous Thromboembolism; Camptothecin; chemotherapy; Risk; Fluorouracil; Case-Control Studies; Gastrointestinal Neoplasms; Middle Aged; venous thromboembolism; Antineoplastic Agents Phytogenic; Femalebusiness

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The effect of CYP3A5 and ABCB1 single nucleotide polymorphisms on tacrolimus dose requirements in Caucasian liver transplant patients

2008

Background: Tacrolimus is a substrate of cytochrome P-450 (CYP) 3A enzyme and of the drug transporter ABCBl. We have investigated the effects of possible relevant CYP3A5 and ABCBl single nucleotide polymorphisms (SNPs) present in both donors and recipients on tacrolimus blood levels achieved in a population of 32 Caucasian liver transplant patients. Material/Methods: At 1, 3 and 6 months after transplantation, tacrolimus doses (mg/kg/day) and trough blood levels (C0) were determined. Polymerase chain reaction followed by restriction fragment length polymorphism analysis was used for gen-otyping CYP3A5*3 [6986A>G] as well as ABCBl at exons 21 [2677G>T] and 26 [3435C>T]. Results:87.5…

MaleCYP3A5ATP Binding Cassette Transporter Subfamily BGenotypeHomozygoteABCB1Polymorphism Single NucleotideTacrolimusWhite PeopleLiver Transplantationliver transplantPharmacogeneticssingle nucleotide polymorphismTacrolimuSettore BIO/14 - FarmacologiaCytochrome P-450 CYP3AHumansFemaleATP Binding Cassette Transporter Subfamily B Member 1Tacrolimus; single nucleotide polymorphisms; CYP3A5; ABCB1; liver transplantImmunosuppressive Agents

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