Featured Publications
Integration of expression QTLs with fine mapping via SuSiE.
Zhang X, Jiang W, Zhao H. Integration of expression QTLs with fine mapping via SuSiE. PLOS Genetics 2024, 20: e1010929. PMID: 38271473, PMCID: PMC10846745, DOI: 10.1371/journal.pgen.1010929.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingGenome-Wide Association StudyLinkage DisequilibriumPhenotypePolymorphism, Single NucleotideQuantitative Trait LociConceptsExpression quantitative trait lociGenome-wide association studiesFine-mapping methodsLinkage disequilibriumBody mass indexFine-mappingExpression quantitative trait loci informationGenome-wide association study resultsExpression quantitative trait loci analysisPresence of linkage disequilibriumExternal reference panelGenetic fine-mappingQuantitative trait lociPosterior inclusion probabilitiesInclusion probabilitiesAlzheimer's diseaseExpression QTLsLD patternsComplex traitsCandidate variantsAssociation studiesTrait lociAssociation to causationReference panelFunctional variants
2023
eQTL studies: from bulk tissues to single cells
Zhang J, Zhao H. eQTL studies: from bulk tissues to single cells. Journal Of Genetics And Genomics 2023, 50: 925-933. PMID: 37207929, PMCID: PMC10656365, DOI: 10.1016/j.jgg.2023.05.003.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression RegulationGenome-Wide Association StudyPolymorphism, Single NucleotideQuantitative Trait LociConceptsExpression quantitative trait lociBulk tissueIdentification of eQTLContext-dependent gene regulationCell typesQuantitative trait lociMost eQTL studiesSingle cellsComplex traitsGene regulationEQTL studiesFunctional genesTrait lociSpecific genesChromosomal regionsDynamic regulationGene expressionBiological processesDifferent tissuesGenetic variantsExpression levelsDisease mechanismsGenesRegulationRecent studies
2020
Leveraging functional annotation to identify genes associated with complex diseases
Liu W, Li M, Zhang W, Zhou G, Wu X, Wang J, Lu Q, Zhao H. Leveraging functional annotation to identify genes associated with complex diseases. PLOS Computational Biology 2020, 16: e1008315. PMID: 33137096, PMCID: PMC7660930, DOI: 10.1371/journal.pcbi.1008315.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociComplex traitsNovel lociIdentification of eQTLGene expressionTranscriptome-wide association study methodLinkage disequilibriumQuantitative trait lociAssociation study methodsCombined Annotation Dependent Depletion (CADD) scoresAnnotation-dependent depletion scoreExpression levelsDisease-associated genesEpigenetic annotationsEpigenetic informationFunctional annotationTrait lociGenetic variationGenesPrevious GWASLociGenetic effectsTraitsComplex diseasesGWASGenome-wide association study of smoking trajectory and meta-analysis of smoking status in 842,000 individuals
Xu K, Li B, McGinnis KA, Vickers-Smith R, Dao C, Sun N, Kember RL, Zhou H, Becker WC, Gelernter J, Kranzler HR, Zhao H, Justice AC. Genome-wide association study of smoking trajectory and meta-analysis of smoking status in 842,000 individuals. Nature Communications 2020, 11: 5302. PMID: 33082346, PMCID: PMC7598939, DOI: 10.1038/s41467-020-18489-3.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesLarge genome-wide association studiesMillion Veteran ProgramAssociation studiesExpression quantitative trait lociQuantitative trait lociChromatin interactionsComplex traitsFunctional annotationTrait lociSequencing ConsortiumDozen genesSignificant lociSmoking phenotypesLociMultiple populationsNew insightsPhenotypeVeteran ProgramGenetic vulnerabilityGenesTraitsAnnotationEuropean AmericansConsortium
2017
A Powerful Approach to Estimating Annotation-Stratified Genetic Covariance via GWAS Summary Statistics
Lu Q, Li B, Ou D, Erlendsdottir M, Powles RL, Jiang T, Hu Y, Chang D, Jin C, Dai W, He Q, Liu Z, Mukherjee S, Crane PK, Zhao H. A Powerful Approach to Estimating Annotation-Stratified Genetic Covariance via GWAS Summary Statistics. American Journal Of Human Genetics 2017, 101: 939-964. PMID: 29220677, PMCID: PMC5812911, DOI: 10.1016/j.ajhg.2017.11.001.Peer-Reviewed Original ResearchConceptsGWAS summary statisticsGenome-wide association studiesComplex traitsSingle nucleotide polymorphismsGenetic covarianceGenetic architectureLarge-scale genome-wide association studiesStrong genetic covarianceDistinct genetic architecturesSignificant genetic covarianceLate-onset Alzheimer's diseaseHigh minor allele frequencyGenetic profileFunctional genomeAmyotrophic lateral sclerosisMajor neurodegenerative diseasesMinor allele frequencyGenetic basisAssociation studiesTraitsLarge-scale inferenceSummary statisticsBiological interpretabilityAllele frequenciesNeurodegenerative diseasesLeveraging functional annotations in genetic risk prediction for human complex diseases
Hu Y, Lu Q, Powles R, Yao X, Yang C, Fang F, Xu X, Zhao H. Leveraging functional annotations in genetic risk prediction for human complex diseases. PLOS Computational Biology 2017, 13: e1005589. PMID: 28594818, PMCID: PMC5481142, DOI: 10.1371/journal.pcbi.1005589.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingData Interpretation, StatisticalData MiningDatabases, GeneticEpigenomicsGenetic Association StudiesGenetic Predisposition to DiseaseGenetic VariationGenome, HumanHumansLinkage DisequilibriumPolymorphism, Single NucleotideProportional Hazards ModelsQuantitative Trait LociRisk AssessmentConceptsGenome-wide association studiesFunctional annotationGenetic risk predictionDisease-associated genetic variantsLinkage disequilibriumIdentification of thousandsWide association studyHuman complex diseasesComplex diseasesGWAS summary statisticsHuman genetics researchAssociation studiesAnnoPredGenotype dataGenetic researchGenetic variantsRelevant variantsAnnotationDisequilibriumMost diseasesDiverse typesSummary statisticsVariantsBayesian frameworkPrecision medicine
2015
Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS
Wang Q, Yang C, Gelernter J, Zhao H. Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS. Human Genetics 2015, 134: 1195-1209. PMID: 26340901, PMCID: PMC4630076, DOI: 10.1007/s00439-015-1596-8.Peer-Reviewed Original ResearchMeSH KeywordsArthritis, RheumatoidCentral Nervous SystemCrohn DiseaseGenetic PleiotropyGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansImmune System DiseasesMental DisordersNerve Tissue ProteinsOrgan SpecificityPolymorphism, Single NucleotideQuantitative Trait LociSchizophreniaSystems IntegrationConceptsImmune disordersPsychiatric disordersCrohn's diseaseDisorder pairsMHC regionPervasive pleiotropyIntegrative analysisGenome-wide association studiesImmune dysregulationImmunological mechanismsTreatment strategiesTraits/diseasesEpidemiological observationsPsychiatric diseasesBrain disordersSame effect directionDiseaseDisordersGenomic regionsRealm of psychiatryMost allelesStrong pleiotropyAnnotation resourcesChromosome 6Association studies