2024
Ancestral origins of TYR and OCA2 gene mutations in oculocutaneous albinism from two admixed populations in Colombia
Cárdenas W, Conley A, Nagar S, Núñez-Ríos D, Jordan I, Lattig M. Ancestral origins of TYR and OCA2 gene mutations in oculocutaneous albinism from two admixed populations in Colombia. PLOS ONE 2024, 19: e0313777. PMID: 39556609, PMCID: PMC11573203, DOI: 10.1371/journal.pone.0313777.Peer-Reviewed Original ResearchConceptsAncestral originTYR haplotypeAdmixed populationsOCA2 geneOCA patientsOCA2 mutationsOculocutaneous albinismAdmixed American populationsDisease-Associated VariantsGlobal reference populationsAutosomal recessive oculocutaneous albinismNative American admixtureDisease-causing mutationsNative American originGene mutationsRecessive conditionColonization historyGenetic architectureGenetic admixtureMendelian diseasesCompound heterozygote patientsAffected family membersAssociation mappingSephardic Jewish originRecessive alleles
2020
Genetic determinants of ammonia-induced acute lung injury in mice
Bein K, Ganguly K, Martin TM, Concel VJ, Brant KA, Di YPP, Upadhyay S, Fabisiak JP, Vuga LJ, Kaminski N, Kostem E, Eskin E, Prows DR, Jang AS, Leikauf GD. Genetic determinants of ammonia-induced acute lung injury in mice. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2020, 320: l41-l62. PMID: 33050709, PMCID: PMC7847062, DOI: 10.1152/ajplung.00276.2020.Peer-Reviewed Original ResearchConceptsSNP associationsWide association mappingGenetic determinantsSignificant SNP associationsAcute lung injuryIntegrative functional approachAssociation mappingMolecular functionsTranscriptomic analysisCandidate genesFunctional domainsNonsynonymous SNPsPromoter regionLung injuryDiverse panelGenesSNPsMouse strainsPathophysiological roleAATFInjuryProteinLAMA3ExpressionAssembly
2015
Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae
Redmond S, Eiglmeier K, Mitri C, Markianos K, Guelbeogo W, Gneme A, Isaacs A, Coulibaly B, Brito-Fravallo E, Maslen G, Mead D, Niare O, Traore S, Sagnon N, Kwiatkowski D, Riehle M, Vernick K. Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae. BMC Genomics 2015, 16: 779. PMID: 26462916, PMCID: PMC4603968, DOI: 10.1186/s12864-015-2009-z.Peer-Reviewed Original ResearchConceptsGenetic mappingFounder coloniesHigh nucleotide diversityNon-model genomesLow linkage disequilibriumPhenotype-genotype mappingPopulation stratificationParasite infection levelsHuman malaria parasiteGenotyping of SNPsNucleotide diversityPooled sequencesAssociation mappingGenomic lociLinkage mappingPlasmodium falciparumSignificant SNPsMosquito systemMarker densityDNA poolsAnopheles gambiaeNatural variationIndividual mosquitoesLinkage disequilibriumSequencing identifies
2013
Functional Genomic Assessment of Phosgene-Induced Acute Lung Injury in Mice
Leikauf GD, Concel VJ, Bein K, Liu P, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA, Upadhyay S, Cario C, Di YP, Vuga LJ, Kostem E, Eskin E, You M, Kaminski N, Prows DR, Knoell DL, Fabisiak JP. Functional Genomic Assessment of Phosgene-Induced Acute Lung Injury in Mice. American Journal Of Respiratory Cell And Molecular Biology 2013, 49: 130522202035005. PMID: 23590305, PMCID: PMC3824050, DOI: 10.1165/rcmb.2012-0337oc.Peer-Reviewed Original ResearchMeSH KeywordsAcute Lung InjuryAllelesAnimalsChemical Warfare AgentsChromosome MappingElectrophoretic Mobility Shift AssayFemaleGene ExpressionGene Expression ProfilingGenomeGenome-Wide Association StudyGenomicsGenotypeIntegrinsLungMiceMice, Inbred StrainsOligonucleotide Array Sequence AnalysisPhosgenePolymorphism, Single NucleotidePromoter Regions, GeneticReelin ProteinSodium-Potassium-Exchanging ATPaseConceptsSignificant SNP associationsSNP associationsTranscriptomic analysisCompetitive electrophoretic mobility shift analysisGenome-wide association mappingFunctional genomic assessmentPutative transcription factorElectrophoretic mobility shift analysisMobility shift analysisAssociation mappingGenetic resolutionTranscription factorsCandidate genesFunctional domainsNonsynonymous SNPsGenomic assessmentPhenotypic differencesPhenotypic extremesDiverse panelGenesGenetic determinantsShift analysisPTPRTAllelesITGA9
2012
Integrative Assessment of Chlorine-Induced Acute Lung Injury in Mice
Leikauf GD, Pope-Varsalona H, Concel VJ, Liu P, Bein K, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA, Upadhyay S, Di YP, Li Q, Hu Z, Vuga LJ, Medvedovic M, Kaminski N, You M, Alexander DC, McDunn JE, Prows DR, Knoell DL, Fabisiak JP. Integrative Assessment of Chlorine-Induced Acute Lung Injury in Mice. American Journal Of Respiratory Cell And Molecular Biology 2012, 47: 234-244. PMID: 22447970, PMCID: PMC3423464, DOI: 10.1165/rcmb.2012-0026oc.Peer-Reviewed Original ResearchConceptsCandidate genesGenetic basisProtein catabolic processAcute lung injuryLung injuryHaplotype association mappingC57BLKS/JSingle nucleotide polymorphism associationsAssociation mappingMetabolomic profilingProtein transportCatabolic processTranscript levelsHaplotype mappingChromosome 1Chlorine-induced acute lung injuryAmino acid carrierSNP associationsReal-time PCRGenesGenetic associationMean survival timeRecognition sitesProfilingPromoter SNPs
2011
Haplotype Association Mapping of Acute Lung Injury in Mice Implicates Activin A Receptor, Type 1
Leikauf GD, Concel VJ, Liu P, Bein K, Berndt A, Ganguly K, Jang AS, Brant KA, Dietsch M, Pope-Varsalona H, Dopico RA, Di YP, Li Q, Vuga LJ, Medvedovic M, Kaminski N, You M, Prows DR. Haplotype Association Mapping of Acute Lung Injury in Mice Implicates Activin A Receptor, Type 1. American Journal Of Respiratory And Critical Care Medicine 2011, 183: 1499-1509. PMID: 21297076, PMCID: PMC3137140, DOI: 10.1164/rccm.201006-0912oc.Peer-Reviewed Original ResearchConceptsDNA-protein bindingHaplotype association mappingSingle nucleotide polymorphism associationsAssociation mappingSNP associationsGenome-wide strategiesPrevious genetic analysisAcute lung injuryAmino acid substitutionsGenomic approachesLung injuryTranscription factorsCell signalingEnriched pathwaysCandidate genesSequence differencesChromosome 1Genetic analysisAssociated variantsAcid substitutionsActivin A receptorsGenesFunctional consequencesPolymorphism associationPolar strains
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