Featured Publications
Set‐based tests for genetic association in longitudinal studies
He Z, Zhang M, Lee S, Smith J, Guo X, Palmas W, Kardia S, Diez Roux A, Mukherjee B. Set‐based tests for genetic association in longitudinal studies. Biometrics 2015, 71: 606-615. PMID: 25854837, PMCID: PMC4601568, DOI: 10.1111/biom.12310.Peer-Reviewed Original ResearchConceptsMulti-Ethnic Study of AtherosclerosisGenome-wide association studiesJoint effect of multiple variantsLinkage disequilibriumAssociation studiesEffects of multiple variantsMarkers of chronic diseaseGenetic variantsSet-based testGene-based testsLongitudinal outcomesMulti-Ethnic StudyGenetic association studiesStudy of AtherosclerosisChronic diseasesPhenotypic variationGenetic associationObservational studyLongitudinal analysisWithin-subject correlationMultiple variantsScore type testsJoint testJoint effectsMarker testsSet-Based Tests for the Gene–Environment Interaction in Longitudinal Studies
He Z, Zhang M, Lee S, Smith J, Kardia S, Roux V, Mukherjee B. Set-Based Tests for the Gene–Environment Interaction in Longitudinal Studies. Journal Of The American Statistical Association 2017, 112: 966-978. PMID: 29780190, PMCID: PMC5954413, DOI: 10.1080/01621459.2016.1252266.Peer-Reviewed Original ResearchGene-environment interactionsMulti-Ethnic Study of AtherosclerosisSet-based testMeasures of neighborhood environmentMarginal genetic associationsEnvironmental exposuresMulti-Ethnic StudyStudy of AtherosclerosisNeighborhood environmentMeasurement of blood pressureGene-environmentMain-effects modelScore type testsMethod of sievesLongitudinal measures of blood pressureRobust to misspecificationGenetic associationGenetic variantsLongitudinal studyMain effectStudy periodEffects modelContinuous environmental exposurePotential biasIndependent conditions
2022
Methods for large‐scale single mediator hypothesis testing: Possible choices and comparisons
Du J, Zhou X, Clark‐Boucher D, Hao W, Liu Y, Smith J, Mukherjee B. Methods for large‐scale single mediator hypothesis testing: Possible choices and comparisons. Genetic Epidemiology 2022, 47: 167-184. PMID: 36465006, PMCID: PMC10329872, DOI: 10.1002/gepi.22510.Peer-Reviewed Original ResearchConceptsNull hypothesisTest statisticsMediation hypothesis testingComposite null hypothesisHypothesis testingClasses of methodsFalse positive rateAlternative hypothesisSimulation studyHypothesis testing methodContinuous mediatorReference distributionSobel test statisticsContinuous outcomesExposure-mediator interactionMulti-Ethnic Study of AtherosclerosisDNA methylation sitesClassCRANMethylation sitesPrediction of telomere length and telomere attrition using a genetic risk score: The multi-ethnic study of atherosclerosis (MESA)
Castro-Diehl C, Smith J, Zhao W, Wang X, Mukherjee B, Seeman T, Needham B. Prediction of telomere length and telomere attrition using a genetic risk score: The multi-ethnic study of atherosclerosis (MESA). Frontiers In Aging 2022, 3: 1021051. PMID: 36304436, PMCID: PMC9592760, DOI: 10.3389/fragi.2022.1021051.Peer-Reviewed Original ResearchMulti-Ethnic Study of AtherosclerosisGenetic risk scoreMulti-Ethnic StudyGenome-wide association studiesStudy of AtherosclerosisAssociated with TLEuropean ancestry genome-wide association studiesEuropean ancestryRisk scoreTL-associated genetic variantsShorter TLEuropean ancestry populationsPredictive of telomere lengthHispanic participantsRace/ethnic groupsLinear mixed effects modelsShorter telomere lengthMixed effects modelsAfrican AmericansTelomere attritionExam 1Association studiesRelative TLTelomere lengthT/S ratioDNA Methylation Mediates the Association Between Individual and Neighborhood Social Disadvantage and Cardiovascular Risk Factors
Wang Y, Zhao W, Ammous F, Song Y, Du J, Shang L, Ratliff S, Moore K, Kelly K, Needham B, Roux A, Liu Y, Butler K, Kardia S, Mukherjee B, Zhou X, Smith J. DNA Methylation Mediates the Association Between Individual and Neighborhood Social Disadvantage and Cardiovascular Risk Factors. Frontiers In Cardiovascular Medicine 2022, 9: 848768. PMID: 35665255, PMCID: PMC9162507, DOI: 10.3389/fcvm.2022.848768.Peer-Reviewed Original ResearchBody mass indexCardiovascular risk factorsNeighborhood socioeconomic disadvantageMulti-Ethnic Study of AtherosclerosisNeighborhood-level disadvantagePoor cardiovascular healthSocioeconomic statusSocioeconomic disadvantageRisk factorsCardiovascular healthAssociated with poor cardiovascular healthSocial disadvantageAdult socioeconomic statusBody mass index adjustmentAssociations of individual-HDL-CPrincipal components of ancestryGenetic principal componentsMeasures of obesityLow socioeconomic statusPopulation-based cohortMulti-Ethnic StudyStudy of AtherosclerosisHDL-C associationHigh-density lipoprotein cholesterol
2021
Bayesian Sparse Mediation Analysis with Targeted Penalization of Natural Indirect Effects
Song Y, Zhou X, Kang J, Aung M, Zhang M, Zhao W, Needham B, Kardia S, Liu Y, Meeker J, Smith J, Mukherjee B. Bayesian Sparse Mediation Analysis with Targeted Penalization of Natural Indirect Effects. Journal Of The Royal Statistical Society Series C (Applied Statistics) 2021, 70: 1391-1412. PMID: 34887595, PMCID: PMC8653861, DOI: 10.1111/rssc.12518.Peer-Reviewed Original ResearchNatural indirect effectMulti-Ethnic Study of AtherosclerosisMediation analysisMediator-outcome effectsMulti-Ethnic StudyStudy of AtherosclerosisCausal mediation analysisLIFECODES birth cohortBirth cohortEpidemiological studiesJoint prior distributionPotential mediatorsHigh-dimensional mediation analysisGaussian mixtureHigh-dimensional mediatorsIndirect effectsPrior distributionEstimation accuracyExposure-mediated effectsBayesian paradigmExposure effectsAvailability of measurementsComposite structuresIncreasing availability of measurementsBayesian hierarchical models for high‐dimensional mediation analysis with coordinated selection of correlated mediators
Song Y, Zhou X, Kang J, Aung M, Zhang M, Zhao W, Needham B, Kardia S, Liu Y, Meeker J, Smith J, Mukherjee B. Bayesian hierarchical models for high‐dimensional mediation analysis with coordinated selection of correlated mediators. Statistics In Medicine 2021, 40: 6038-6056. PMID: 34404112, PMCID: PMC9257993, DOI: 10.1002/sim.9168.Peer-Reviewed Original Research
2020
Social regulation of inflammation related gene expression in the multi-ethnic study of atherosclerosis
Brown K, Diez-Roux A, Smith J, Needham B, Mukherjee B, Ware E, Liu Y, Cole S, Seeman T, Kardia S. Social regulation of inflammation related gene expression in the multi-ethnic study of atherosclerosis. Psychoneuroendocrinology 2020, 117: 104654. PMID: 32387875, PMCID: PMC7685527, DOI: 10.1016/j.psyneuen.2020.104654.Peer-Reviewed Original ResearchConceptsGene expressionMulti-Ethnic Study of AtherosclerosisGene set enrichment testGene Ontology databaseGene expression dataMulti-Ethnic StudyLifetime discriminationStudy of AtherosclerosisDifferential gene expressionInflammation-related genesExpression dataGene setsChronic burdenSocial factorsGene transcriptionRelated gene expressionOntology databaseGenesInflammatory responseTranscriptionGlobal analysisElastic net penalized regressionAdverse social factorsGlobal expressionExpression of inflammation-related genes
2017
Rare‐variant association tests in longitudinal studies, with an application to the Multi‐Ethnic Study of Atherosclerosis (MESA)
He Z, Lee S, Zhang M, Smith J, Guo X, Palmas W, Kardia S, Ionita‐Laza I, Mukherjee B. Rare‐variant association tests in longitudinal studies, with an application to the Multi‐Ethnic Study of Atherosclerosis (MESA). Genetic Epidemiology 2017, 41: 801-810. PMID: 29076270, PMCID: PMC5696115, DOI: 10.1002/gepi.22081.Peer-Reviewed Original ResearchConceptsMulti-Ethnic Study of AtherosclerosisMulti-Ethnic StudyStudy of AtherosclerosisType I error rateRare-variant association testsRare variantsGene-based association testsRare-variant associationsAssociation TestLongitudinal outcomesLongitudinal studyExome sequencing dataMeasurement of blood pressureGenomic regionsSequence dataTrait heritabilitySequencing studiesMeasured outcomesGenetic variantsVariant analysisModerate sample sizesIndividual variantsRobust to misspecificationWithin-subject correlationStatistical powerNeighborhood characteristics influence DNA methylation of genes involved in stress response and inflammation: The Multi-Ethnic Study of Atherosclerosis
Smith J, Zhao W, Wang X, Ratliff S, Mukherjee B, Kardia S, Liu Y, Roux A, Needham B. Neighborhood characteristics influence DNA methylation of genes involved in stress response and inflammation: The Multi-Ethnic Study of Atherosclerosis. Epigenetics 2017, 12: 662-673. PMID: 28678593, PMCID: PMC5687339, DOI: 10.1080/15592294.2017.1341026.Peer-Reviewed Original ResearchConceptsMulti-Ethnic Study of AtherosclerosisMulti-Ethnic StudyStudy of AtherosclerosisSocioeconomic disadvantageIndividual-level socioeconomic factorsEtiology of health disparitiesAssociated with poor health outcomesPopulation-based sample of US adultsSocioeconomic factorsNeighborhood conditionsNeighborhood socioeconomic disadvantageSample of US adultsNeighborhood social environmentHigher socioeconomic disadvantagePoor health outcomesIndividual socioeconomic factorsPopulation-based sampleDimensions of neighborhood contextHealth disparitiesInfluence methylation levelsHealth outcomesUS adultsSocial environmentDisadvantaged neighborhoodsNeighborhood characteristics
2015
Comparative genome-wide association studies of a depressive symptom phenotype in a repeated measures setting by race/ethnicity in the multi-ethnic study of atherosclerosis
Ware E, Mukherjee B, Sun Y, Diez-Roux A, Kardia S, Smith J. Comparative genome-wide association studies of a depressive symptom phenotype in a repeated measures setting by race/ethnicity in the multi-ethnic study of atherosclerosis. BMC Genomic Data 2015, 16: 118. PMID: 26459564, PMCID: PMC4603946, DOI: 10.1186/s12863-015-0274-0.Peer-Reviewed Original ResearchConceptsMulti-Ethnic StudyGenome-wide association studiesStudies of depressive symptomsMulti-Ethnic Study of AtherosclerosisDepressive symptomsStudy of AtherosclerosisGenome-wide suggestive levelMeasures analysisSingle-nucleotide polymorphismsMultiple ethnicitiesBaseline measurementsMeta-analysisEuropean AmericansLongitudinal measurementsGenome-wide analysisLongitudinal frameworkSuggestive levelAssociation studiesMethodsThis studyEthnicityGenetic predictorsP-valueMood disordersHealthNovel variantsLife course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: The multi-ethnic study of atherosclerosis
Needham B, Smith J, Zhao W, Wang X, Mukherjee B, Kardia S, Shively C, Seeman T, Liu Y, Roux A. Life course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: The multi-ethnic study of atherosclerosis. Epigenetics 2015, 10: 958-969. PMID: 26295359, PMCID: PMC4844216, DOI: 10.1080/15592294.2015.1085139.Peer-Reviewed Original ResearchConceptsMulti-Ethnic Study of AtherosclerosisAssociated with DNA methylationSocioeconomic statusStress-related genesMulti-Ethnic StudyStudy of AtherosclerosisDNA methylationLow adult socioeconomic statusLife course socioeconomic statusLow childhood socioeconomic statusMeasures of socioeconomic statusAdult socioeconomic statusSocial patterning of diseaseChildhood socioeconomic statusGene expressionLow socioeconomic statusLife course measuresAssociated with gene expressionInflammation-related genesFunctional consequences of alterationsDNA methylation measurementsNon-HispanicHispanic participantsPotential functional consequencesEpigenetic dataApplying Novel Methods for Assessing Individual- and Neighborhood-Level Social and Psychosocial Environment Interactions with Genetic Factors in the Prediction of Depressive Symptoms in the Multi-Ethnic Study of Atherosclerosis
Ware E, Smith J, Mukherjee B, Lee S, Kardia S, Diez-Roux A. Applying Novel Methods for Assessing Individual- and Neighborhood-Level Social and Psychosocial Environment Interactions with Genetic Factors in the Prediction of Depressive Symptoms in the Multi-Ethnic Study of Atherosclerosis. Behavior Genetics 2015, 46: 89-99. PMID: 26254610, PMCID: PMC4720563, DOI: 10.1007/s10519-015-9734-6.Peer-Reviewed Original ResearchConceptsDepressive symptom scoresMulti-Ethnic Study of AtherosclerosisGene regionNeighborhood levelMulti-Ethnic StudyPredictive of depressive symptomsStudy of AtherosclerosisMultiple race/ethnicitiesMultiple testing correctionAssess individual-SKAT analysisNeighborhood factorsEtiology of depressive illnessDepressive symptomsPsychosocial stressorsSymptom scoresComplex illnessTesting correctionRace/ethnicityRace/ethnicitiesEthnic groupsDepressive illnessGenetic predispositionIndividual-Genetic factorsAssociation between Stress Response Genes and Features of Diurnal Cortisol Curves in the Multi-Ethnic Study of Atherosclerosis: A New Multi-Phenotype Approach for Gene-Based Association Tests
He Z, Payne E, Mukherjee B, Lee S, Smith J, Ware E, Sánchez B, Seeman T, Kardia S, Roux A. Association between Stress Response Genes and Features of Diurnal Cortisol Curves in the Multi-Ethnic Study of Atherosclerosis: A New Multi-Phenotype Approach for Gene-Based Association Tests. PLOS ONE 2015, 10: e0126637. PMID: 25993632, PMCID: PMC4439141, DOI: 10.1371/journal.pone.0126637.Peer-Reviewed Original ResearchConceptsMulti-Ethnic Study of AtherosclerosisMarker association testsCortisol featuresMulti-Ethnic StudySingle marker association testsStudy of AtherosclerosisAssociation TestGene level association testsGene-based association testsEthnic-specific resultsMeta-analysisGenetic contribution to variabilityGene-level analysisStress-responsive genesSample of European AmericansGenotype-phenotype associationsDiurnal cortisol curveHispanic AmericansChronic diseasesMultiple physiological systemsDaily cortisol profilesAfrican AmericansGene approachGene-basedMultiple testing
2014
Testing departure from additivity in Tukey's model using shrinkage: application to a longitudinal setting
Ko Y, Mukherjee B, Smith J, Park S, Kardia S, Allison M, Vokonas P, Chen J, Diez‐Roux A. Testing departure from additivity in Tukey's model using shrinkage: application to a longitudinal setting. Statistics In Medicine 2014, 33: 5177-5191. PMID: 25112650, PMCID: PMC4227925, DOI: 10.1002/sim.6281.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overAgingAtherosclerosisBone and BonesComputer SimulationEnvironmental ExposureEthnicityFemaleGene-Environment InteractionHumansIronLeadLeast-Squares AnalysisLikelihood FunctionsLongitudinal StudiesMaleMiddle AgedModels, GeneticUnited StatesUnited States Department of Veterans AffairsConceptsGene-environment interactionsMulti-Ethnic Study of AtherosclerosisModel of gene-environment interactionMulti-Ethnic StudyTukey's modelLongitudinal settingStudy of AtherosclerosisNormative Aging StudyCase-control studyIncreasing categoriesAging StudyTested interactionsLongitudinal studyCategorical variablesRobust to misspecificationInteraction termsTest departuresShrinkage estimatorsWald testInteraction estimatesIncreased powerOne-degree-of-freedom modelInteraction effectsSetsEnvironmental markers