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
2019
A Fast and Accurate Method for Genome-wide Scale Phenome-wide G × E Analysis and Its Application to UK Biobank
Bi W, Zhao Z, Dey R, Fritsche L, Mukherjee B, Lee S. A Fast and Accurate Method for Genome-wide Scale Phenome-wide G × E Analysis and Its Application to UK Biobank. American Journal Of Human Genetics 2019, 105: 1182-1192. PMID: 31735295, PMCID: PMC6904814, DOI: 10.1016/j.ajhg.2019.10.008.Peer-Reviewed Original ResearchConceptsCase-control ratioGenome-wide significance levelMeasures of environmental exposureGenome-wide analysisEuropean ancestry samplesGenetic association studiesSaddlepoint approximationCase-control imbalanceAnalysis of phenotypesGene-environment interactionsPopulation-based biobanksControlled type I error ratesAssociation studiesG x E effectsUK BiobankType I error rateGenetic variantsE analysisSPAGEComplex diseasesEnvironmental exposuresTest statisticsE studySimulation studyWald testA comprehensive gene–environment interaction analysis in Ovarian Cancer using genome‐wide significant common variants
Kim S, Wang M, Tyrer J, Jensen A, Wiensch A, Liu G, Lee A, Ness R, Salvatore M, Tworoger S, Whittemore A, Anton‐Culver H, Sieh W, Olson S, Berchuck A, Goode E, Goodman M, Doherty J, Chenevix‐Trench G, Rossing M, Webb P, Giles G, Terry K, Ziogas A, Fortner R, Menon U, Gayther S, Wu A, Song H, Brooks‐Wilson A, Bandera E, Cook L, Cramer D, Milne R, Winham S, Kjaer S, Modugno F, Thompson P, Chang‐Claude J, Harris H, Schildkraut J, Le N, Wentzensen N, Trabert B, Høgdall E, Huntsman D, Pike M, Pharoah P, Pearce C, Mukherjee B. A comprehensive gene–environment interaction analysis in Ovarian Cancer using genome‐wide significant common variants. International Journal Of Cancer 2019, 144: 2192-2205. PMID: 30499236, PMCID: PMC6399057, DOI: 10.1002/ijc.32029.Peer-Reviewed Original ResearchConceptsOral contraceptive pill useExcess risk due to additive interactionOvarian cancer risk factorsOral contraceptive pillsGene-environment interaction analysisCancer risk factorsGene-environment analysisOvarian cancer casesOCP useCase-control studyGenome-wide association analysisAdditive scaleCancer casesOvarian cancerOdds ratioCommon variantsDuration of OCP useRisk allelesRisk factorsGenetic variantsAdditive interactionAssociation analysisWomenFollow-upC allele
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
Genome-wide association study of colorectal cancer identifies six new susceptibility loci
Schumacher FR, Schmit SL, Jiao S, Edlund CK, Wang H, Zhang B, Hsu L, Huang SC, Fischer CP, Harju JF, Idos GE, Lejbkowicz F, Manion FJ, McDonnell K, McNeil CE, Melas M, Rennert HS, Shi W, Thomas DC, Van Den Berg DJ, Hutter CM, Aragaki AK, Butterbach K, Caan BJ, Carlson CS, Chanock SJ, Curtis KR, Fuchs CS, Gala M, Giovannucci EL, Gogarten SM, Hayes RB, Henderson B, Hunter DJ, Jackson RD, Kolonel LN, Kooperberg C, Küry S, LaCroix A, Laurie CC, Laurie CA, Lemire M, Levine D, Ma J, Makar KW, Qu C, Taverna D, Ulrich CM, Wu K, Kono S, West DW, Berndt SI, Bezieau S, Brenner H, Campbell PT, Chan AT, Chang-Claude J, Coetzee GA, Conti DV, Duggan D, Figueiredo JC, Fortini BK, Gallinger SJ, Gauderman WJ, Giles G, Green R, Haile R, Harrison TA, Hoffmeister M, Hopper JL, Hudson TJ, Jacobs E, Iwasaki M, Jee SH, Jenkins M, Jia WH, Joshi A, Li L, Lindor NM, Matsuo K, Moreno V, Mukherjee B, Newcomb PA, Potter JD, Raskin L, Rennert G, Rosse S, Severi G, Schoen RE, Seminara D, Shu XO, Slattery ML, Tsugane S, White E, Xiang YB, Zanke BW, Zheng W, Le Marchand L, Casey G, Gruber SB, Peters U. Genome-wide association study of colorectal cancer identifies six new susceptibility loci. Nature Communications 2015, 6: 7138. PMID: 26151821, PMCID: PMC4967357, DOI: 10.1038/ncomms8138.Peer-Reviewed Original ResearchConceptsNew susceptibility lociAssociation studiesSusceptibility lociSignificant genetic lociGenome-wide association studiesGenome-wide thresholdCommon genetic variantsRare pathogenic mutationsTwo-stage association studyGenetic lociGenetic epidemiology studiesGenetic variantsLociUnderlying biological mechanismsPathogenic mutationsBiological mechanismsAsian ConsortiumGenetic susceptibilityMutationsAdditional insightColorectal cancerCancerVariants