2022
Incorporating family disease history and controlling case–control imbalance for population-based genetic association studies
Zhuang Y, Wolford B, Nam K, Bi W, Zhou W, Willer C, Mukherjee B, Lee S. Incorporating family disease history and controlling case–control imbalance for population-based genetic association studies. Bioinformatics 2022, 38: 4337-4343. PMID: 35876838, PMCID: PMC9477535, DOI: 10.1093/bioinformatics/btac459.Peer-Reviewed Original ResearchConceptsEmpirical saddlepoint approximationFamily disease historyCase-control imbalanceSaddlepoint approximationGenome-wide association analysisPopulation-based genetic association studiesGenetic association testsVariant-phenotype associationsDisease historyGenetic association studiesLow detection powerType I error inflationCorrelation of phenotypesWhite British sampleSupplementary dataAssociation studiesPopulation-based biobanksIncreased phenotypic correlationsKorean GenomeSimulation studyPhenotype distributionPhenotypeAssociation TestBioinformaticsPhenotypic correlations
2021
Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes
Bi W, Zhou W, Dey R, Mukherjee B, Sampson J, Lee S. Efficient mixed model approach for large-scale genome-wide association studies of ordinal categorical phenotypes. American Journal Of Human Genetics 2021, 108: 825-839. PMID: 33836139, PMCID: PMC8206161, DOI: 10.1016/j.ajhg.2021.03.019.Peer-Reviewed Original ResearchConceptsOrdinal categorical phenotypesGenome-wide association studiesCategorical phenotypesGenome-wide significant variantsRare variantsPhenotype distributionControlled type I error ratesType I error rateMixed model approachArray genotypingAssociation studiesCommon variantsQuantitative traitsSignificant variantsLogistic mixed modelsLack of analysis toolsUK BiobankLinear mixed model approachPhenotypeAssociation TestVariantsMixed modelsSignificance levelMAFTraits
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 power
2015
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
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
2009
Shrinkage estimation for robust and efficient screening of single‐SNP association from case‐control genome‐wide association studies
Luo S, Mukherjee B, Chen J, Chatterjee N. Shrinkage estimation for robust and efficient screening of single‐SNP association from case‐control genome‐wide association studies. Genetic Epidemiology 2009, 33: 740-750. PMID: 19434716, PMCID: PMC3103068, DOI: 10.1002/gepi.20428.Peer-Reviewed Original ResearchMeSH KeywordsCase-Control StudiesComputational BiologyComputer SimulationData Interpretation, StatisticalFalse Positive ReactionsGenetic MarkersGenomeGenome, HumanGenome-Wide Association StudyGenotypeHumansLikelihood FunctionsModels, StatisticalPolymorphism, Single NucleotideReproducibility of ResultsConceptsHardy-Weinberg equilibriumAssociation TestPopulation-based case-control designGenome-wide association scanGenome-wide association studiesSingle-SNP associationsCase-control designCase-control studyAssociation scansAssociation studiesGenetic markersSusceptibility SNPsRecessive effectUnderlying populationAssociationFalse-positive resultsEfficient screeningSNPsRare diseaseShrinkage estimatorsSimulation studyStudyTestTwo-degrees-of-freedomPopulation