2023
Multi‐omics cannot replace sample size in genome‐wide association studies
Baranger D, Hatoum A, Polimanti R, Gelernter J, Edenberg H, Bogdan R, Agrawal A. Multi‐omics cannot replace sample size in genome‐wide association studies. Genes Brain & Behavior 2023, 22: e12846. PMID: 36977197, PMCID: PMC10733567, DOI: 10.1111/gbb.12846.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression ProfilingGenome-Wide Association StudyMultiomicsPhenotypePolymorphism, Single NucleotideSample SizeConceptsGenome-wide association studiesLarge genome-wide association studiesNovel genesMulti-omics dataMulti-omics informationAssociation studiesGenome-wide significant lociSmall genome-wide association studyBrain-related traitsGWAS sample sizesEarly genome-wide association studiesNovel gene discoveryGene discoverySignificant lociAdditional genesPositional mappingHeritable traitVariant discoverySimilar traitsGenesNovel variant discoveryTraitsDisease biologyLociDiscovery
2019
Genomewide Gene-by-Sex Interaction Scans Identify ADGRV1 for Sex Differences in Opioid Dependent African Americans
Yang BZ, Zhou H, Cheng Z, Kranzler HR, Gelernter J. Genomewide Gene-by-Sex Interaction Scans Identify ADGRV1 for Sex Differences in Opioid Dependent African Americans. Scientific Reports 2019, 9: 18070. PMID: 31792237, PMCID: PMC6889277, DOI: 10.1038/s41598-019-53560-0.Peer-Reviewed Original ResearchMeSH KeywordsAdultAllelesAnalgesics, OpioidBlack or African AmericanBrainCalcium-Binding ProteinsFemaleGene Expression ProfilingGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMaleMiddle AgedOpioid-Related DisordersPolymorphism, Single NucleotideReceptors, G-Protein-CoupledReceptors, Kainic AcidSex FactorsWhite PeopleConceptsOpioid dependenceOD riskSex-different effectsSex differencesInferior olivary nucleusDSM-IV diagnosisDimorphic riskSubstantia nigraAA menOlivary nucleusFrontal cortexEuropean-American subjectsADGRV1Further studiesRiskAfrican AmericansGenetic variantsDisease enrichment analysisBrainSex interactionNominal significanceMenFirst studyPutamenLungAlcohol-responsive genes identified in human iPSC-derived neural cultures
Jensen KP, Lieberman R, Kranzler HR, Gelernter J, Clinton K, Covault J. Alcohol-responsive genes identified in human iPSC-derived neural cultures. Translational Psychiatry 2019, 9: 96. PMID: 30862775, PMCID: PMC6414668, DOI: 10.1038/s41398-019-0426-5.Peer-Reviewed Original ResearchConceptsAlcohol-responsive genesGene expressionGene regulatory effectsTotal RNA sequencingCo-expressed genesNeural cell culturesCholesterol biosynthesis pathwayPrimary neural tissueCorrelation network analysisHuman-induced pluripotent stem cellsPluripotent stem cellsBiosynthesis pathwayCell culturesResponsive genesRNA sequencingNotch signalingEnrichment analysisMolecular mechanismsCell cycleAlcohol exposureGenesCell culture modelGenetic effectsCholesterol homeostasisStem cells
2017
Widespread signatures of positive selection in common risk alleles associated to autism spectrum disorder
Polimanti R, Gelernter J. Widespread signatures of positive selection in common risk alleles associated to autism spectrum disorder. PLOS Genetics 2017, 13: e1006618. PMID: 28187187, PMCID: PMC5328401, DOI: 10.1371/journal.pgen.1006618.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAttention Deficit Disorder with HyperactivityAutism Spectrum DisorderBipolar DisorderBrainComputational BiologyDepressive Disorder, MajorGene Expression ProfilingGene OntologyGene Regulatory NetworksGenetic Predisposition to DiseaseGenome-Wide Association StudyGenomicsHumansPituitary GlandPolymorphism, Single NucleotideRisk FactorsSchizophreniaTranscriptomeConceptsPositive selectionGene Ontology enrichmentGene expression enrichmentPrevious genetic studiesGWAS summary statisticsNervous system developmentCommon risk allelesPsychiatric Genomics ConsortiumSystems geneticsOntology enrichmentRisk allelesSynapse organizationWidespread signaturesEvolutionary processesGenetic studiesGenomics ConsortiumGWASHuman evolutionAllelesIncomplete selectionEffect directionMinor alleleComplete selectionEnrichmentSummary statistics
2016
DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders
Wang F, Xu H, Zhao H, Gelernter J, Zhang H. DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders. Scientific Reports 2016, 6: 19430. PMID: 26763658, PMCID: PMC4725922, DOI: 10.1038/srep19430.Peer-Reviewed Original ResearchConceptsCo-methylation modulesPostmortem prefrontal cortex tissueDNA methylome alterationsCo-methylation analysisDNA methylation alterationsSubstance dependence phenotypesTranscriptional regulationDNA methylomeMethylation alterationsMethylome alterationsBiological processesPostmortem prefrontal cortexExpression relationshipsNeural developmentDifferential expressionPrefrontal cortex tissueGenesDependence phenotypesMultiple testing correctionCpGAUD subjectsFemale pairsCortex tissueMethylomePhenotype
2014
Differentially co-expressed genes in postmortem prefrontal cortex of individuals with alcohol use disorders: influence on alcohol metabolism-related pathways
Zhang H, Wang F, Xu H, Liu Y, Liu J, Zhao H, Gelernter J. Differentially co-expressed genes in postmortem prefrontal cortex of individuals with alcohol use disorders: influence on alcohol metabolism-related pathways. Human Genetics 2014, 133: 1383-1394. PMID: 25073604, PMCID: PMC4185230, DOI: 10.1007/s00439-014-1473-x.Peer-Reviewed Original ResearchConceptsCo-expressed genesGenome-wide association studiesHumanHT-12 v4 Expression BeadChipGene modulesPostmortem prefrontal cortexGene co-expression network analysisCo-expression network analysisDAVID Bioinformatics ResourcesGene expression alterationsMetabolism-related pathwaysV4 Expression BeadChipCellular functionsTranscriptome profilesFatty acid metabolismBioinformatics resourcesEnrichment analysisExpression probesBiological pathwaysAssociation studiesAldehyde detoxificationExpression alterationsGenesMitochondrial functionBrain reward regionsAcid metabolism
2013
Sex-biased methylome and transcriptome in human prefrontal cortex
Xu H, Wang F, Liu Y, Yu Y, Gelernter J, Zhang H. Sex-biased methylome and transcriptome in human prefrontal cortex. Human Molecular Genetics 2013, 23: 1260-1270. PMID: 24163133, PMCID: PMC3919013, DOI: 10.1093/hmg/ddt516.Peer-Reviewed Original ResearchConceptsDNA methylationGene expressionSex-biased DNA methylationMultiple test correctionGenome-wide DNA methylationGene Ontology annotationsDAVID functional annotation analysisFunctional annotation analysisRibosome structurePhenotypic variationAnnotation analysisGO termsProtein translationRNA bindingOntology annotationsHost genesDifferential methylationExpression correlationTranscriptomic profilesDifferential brain developmentDifferential expressionMethylation levelsGenesMethylationTranscriptome
2011
Genome-Wide Association Study of Alcohol Dependence Implicates KIAA0040 on Chromosome 1q
Zuo L, Gelernter J, Zhang CK, Zhao H, Lu L, Kranzler HR, Malison RT, Li CS, Wang F, Zhang XY, Deng HW, Krystal JH, Zhang F, Luo X. Genome-Wide Association Study of Alcohol Dependence Implicates KIAA0040 on Chromosome 1q. Neuropsychopharmacology 2011, 37: 557-566. PMID: 21956439, PMCID: PMC3242317, DOI: 10.1038/npp.2011.229.Peer-Reviewed Original ResearchConceptsSignificant risk genesHapMap populationsGenome-wide association analysisExpression quantitative trait loci (eQTL) analysisGenome-wide association study data setsQuantitative trait locus (QTL) analysisAssociation analysisMetabolic pathwaysRisk genesGenome-wide association studiesSNP-expression associationsCis-acting regulatory effectsExtracellular matrix proteinsGene expression levelsNumerous genesSignificant SNPsCausal variantsKIAA0040Risk lociRisk of ADLocus analysisAssociation studiesMatrix proteinsRisk SNPsCell migration