2021
powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis
Dong X, Li X, Chang T, Scherzer C, Weiss S, Qiu W. powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis. Bioinformatics 2021, 37: 4269-4271. PMID: 34009297, PMCID: PMC9492284, DOI: 10.1093/bioinformatics/btab385.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociGenome-wide association studiesEQTL analysisDetectable minor allele frequencyExpression quantitative trait loci analysisAllele frequenciesGene expressionPost-GWAS eraAssociated with gene expressionQuantitative trait lociR packageMinor allele frequencySingle-cell dataEstimate statistical powerSupplementary dataGenetic lociTrait lociAssociation studiesR Shiny applicationGenetic variationSample sizeGenetic variantsLociBioinformaticsShiny application
2018
Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer
Walsh N, Zhang H, Hyland PL, Yang Q, Mocci E, Zhang M, Childs EJ, Collins I, Wang Z, Arslan AA, Beane-Freeman L, Bracci PM, Brennan P, Canzian F, Duell EJ, Gallinger S, Giles GG, Goggins M, Goodman GE, Goodman PJ, Hung RJ, Kooperberg C, Kurtz RC, Malats N, LeMarchand L, Neale RE, Olson SH, Scelo G, Shu XO, Van Den Eeden SK, Visvanathan K, White E, Zheng W, consortia P, Albanes D, Andreotti G, Babic A, Bamlet W, Berndt S, Borgida A, Boutron-Ruault M, Brais L, Brennan P, Bueno-de-Mesquita B, Buring J, Chaffee K, Chanock S, Cleary S, Cotterchio M, Foretova L, Fuchs C, Gaziano J, Giovannucci E, Goggins M, Hackert T, Haiman C, Hartge P, Hasan M, Helzlsouer K, Herman J, Holcatova I, Holly E, Hoover R, Hung R, Janout V, Klein E, Kurtz R, Laheru D, Lee I, Lu L, Malats N, Mannisto S, Milne R, Oberg A, Orlow I, Patel A, Peters U, Porta M, Real F, Rothman N, Sesso H, Severi G, Silverman D, Strobel O, Sund M, Thornquist M, Tobias G, Wactawski-Wende J, Wareham N, Weiderpass E, Wentzensen N, Wheeler W, Yu H, Zeleniuch-Jacquotte A, Kraft P, Li D, Jacobs E, Petersen G, Wolpin B, Risch H, Amundadottir L, Yu K, Klein A, Stolzenberg-Solomon R. Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer. Journal Of The National Cancer Institute 2018, 111: 557-567. PMID: 30541042, PMCID: PMC6579744, DOI: 10.1093/jnci/djy155.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGene setsSingle nucleotide polymorphismsFunctional annotationEpidermal growth factor receptor transactivationExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisGrowth factor receptor transactivationTop single nucleotide polymorphismsG protein-coupled receptorsGene-set analysisProtein-coupled receptorsIndividual single nucleotide polymorphismsBeta-cell developmentEQTL analysisGWAS dataPCC genesPancreatic ductal adenocarcinomaReceptor transactivationLocus analysisPathway analysisAssociation studiesGenesSusceptibility genesIdentifies associations
2017
10 Single cell expression quantitative trait LOCI (EQTL) analsis of established lupus-risk loci in patient monocytes
Ghodke-Puranik Y, Zhongbo J, Fan W, Jensen M, Dorschner J, Vsetecka D, Amin S, Makol A, Ernste F, Osborn T, Moder K, Chowdhary V, Niewold T. 10 Single cell expression quantitative trait LOCI (EQTL) analsis of established lupus-risk loci in patient monocytes. Lupus Science & Medicine 2017, 4: a6. DOI: 10.1136/lupus-2017-000215.10.Peer-Reviewed Original ResearchCell typesFluidigm C1 systemDifferent cellular eventsRelated cell typesSLE risk lociDifferent cell typesEQTL associationsLoci interactEQTL analysisGene expressionMajor unanswered questionSingle-cell captureCellular eventsLoci influenceSame SNPLociPleiotropic effectsGenesEQTLsSPP1SNPsC1 systemLimited overlapImmune cell typesImmune system function
2016
Replicated Risk Nicotinic Cholinergic Receptor Genes for Nicotine Dependence
Zuo L, Garcia-Milian R, Guo X, Zhong C, Tan Y, Wang Z, Wang J, Wang X, Kang L, Lu L, Chen X, Li CR, Luo X. Replicated Risk Nicotinic Cholinergic Receptor Genes for Nicotine Dependence. Genes 2016, 7: 95. PMID: 27827986, PMCID: PMC5126781, DOI: 10.3390/genes7110095.Peer-Reviewed Original ResearchNicotinic cholinergic receptor genesRisk genesRisk variantsCholinergic receptor genesReceptor geneMouse brainGenomic regionsEQTL analysisBioinformatics analysisProtein structureNicotinic acetylcholine receptorsGenesMouse brain samplesGenetic variantsAcetylcholine receptorsIndependent humanExpressionPotential functionVariantsImportant roleSplicingTranscriptionBrain samplesCHRNA5-A3RNA
2012
Genome‐wide search for replicable risk gene regions in alcohol and nicotine co‐dependence
Zuo L, Zhang F, Zhang H, Zhang X, Wang F, Li C, Lu L, Hong J, Lu L, Krystal J, Deng H, Luo X. Genome‐wide search for replicable risk gene regions in alcohol and nicotine co‐dependence. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2012, 159B: 437-444. PMID: 22488850, PMCID: PMC3405545, DOI: 10.1002/ajmg.b.32047.Peer-Reviewed Original ResearchConceptsChromosome 3Genome-wide false discovery rateGene regionFalse discovery rateGenome-wide association analysisExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisRisk SNPsTranscript expressionGenome-wide association strategyGenome-wide searchCombined P valueSNP-disease associationsAssociation peakGenomic regionsEQTL analysisEuropean American casesCausal lociLocus analysisGene expressionAssociation analysisGenesSNPsRegulatory effectsDiscovery rate
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