Featured Publications
Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative
Fritsche L, Gruber S, Wu Z, Schmidt E, Zawistowski M, Moser S, Blanc V, Brummett C, Kheterpal S, Abecasis G, Mukherjee B. Association of Polygenic Risk Scores for Multiple Cancers in a Phenome-wide Study: Results from The Michigan Genomics Initiative. American Journal Of Human Genetics 2018, 102: 1048-1061. PMID: 29779563, PMCID: PMC5992124, DOI: 10.1016/j.ajhg.2018.04.001.Peer-Reviewed Original ResearchConceptsPolygenic risk scoresElectronic health recordsAssociations of polygenic risk scoresPhenome-wide significant associationsPolygenic risk score associationsLongitudinal biorepository effortNon-cancer diagnosesPatients' electronic health recordsPhenome-wide association studyAnalysis of temporal orderMichigan Genomics InitiativeRisk scoreAssociated with multiple phenotypesFemale breast cancerNHGRI-EBI CatalogRisk profileGenetic risk profilesMeasures of genomic variationCancer traitsCase-control studyPheWAS analysisHealth recordsHealth systemMichigan MedicineCancer diagnosisCharacteristics Associated With Racial/Ethnic Disparities in COVID-19 Outcomes in an Academic Health Care System
Gu T, Mack J, Salvatore M, Sankar S, Valley T, Singh K, Nallamothu B, Kheterpal S, Lisabeth L, Fritsche L, Mukherjee B. Characteristics Associated With Racial/Ethnic Disparities in COVID-19 Outcomes in an Academic Health Care System. JAMA Network Open 2020, 3: e2025197. PMID: 33084902, PMCID: PMC7578774, DOI: 10.1001/jamanetworkopen.2020.25197.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedBetacoronavirusBlack or African AmericanComorbidityCoronavirus InfectionsCOVID-19Diabetes Mellitus, Type 2FemaleHealth Status DisparitiesHospitalizationHumansIntensive Care UnitsKidney DiseasesMaleMichiganMiddle AgedNeoplasmsObesityOdds RatioPandemicsPneumonia, ViralPopulation DensityRetrospective StudiesRisk FactorsSARS-CoV-2White PeopleConceptsAssociated with higher riskInternational Classification of DiseasesRisk of hospitalizationPreexisting type 2 diabetesHigher risk of hospitalizationClassification of DiseasesType 2 diabetesCOVID-19 outcomesRacial/ethnic disparitiesWhite patientsBlack patientsIntensive care unitInternational ClassificationResidential-level socioeconomic characteristicsOdds ratioStatistically significant racial differencesHigh riskAssociated with higher risk of hospitalizationNon-Hispanic blacksAssociation of risk factorsNon-Hispanic whitesMichigan Department of HealthAssociated with increased risk of hospitalizationComorbidity scoreDepartment of HealthIncorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction
Zhuang Y, Kim N, Fritsche L, Mukherjee B, Lee S. Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction. BMC Bioinformatics 2024, 25: 65. PMID: 38336614, PMCID: PMC11323637, DOI: 10.1186/s12859-024-05664-2.Peer-Reviewed Original ResearchConceptsPredictive performance of polygenic risk scoresFunctional annotationGenetic architecturePerformance of polygenic risk scoresPRS-CSAnnotation informationPolygenic risk predictionGenetic risk predictionPolygenic risk scoresFunctional annotation informationKyoto Encyclopedia of GenesRisk predictionProportion of variantsEncyclopedia of GenesGenomes (KEGGSource of annotationTrait heritabilityAnnotation groupsPathway informationQuantitative traitsKyoto EncyclopediaFunctional categoriesBackgroundGenetic variantsHeritable contributionReal world data sourcesRisk of Non-Melanoma Cancers in First-Degree Relatives of CDKN2A Mutation Carriers
Mukherjee B, DeLancey J, Raskin L, Everett J, Jeter J, Begg C, Orlow I, Berwick M, Armstrong B, Kricker A, Marrett L, Millikan R, Culver H, Rosso S, Zanetti R, Kanetsky P, From L, Gruber S, Investigators F. Risk of Non-Melanoma Cancers in First-Degree Relatives of CDKN2A Mutation Carriers. Journal Of The National Cancer Institute 2012, 104: 953-956. PMID: 22534780, PMCID: PMC3379723, DOI: 10.1093/jnci/djs221.Peer-Reviewed Original ResearchConceptsFirst-degree relatives of carriersCDKN2A mutation carriersFirst-degree relativesMutation carriersNon-melanoma cancersFirst-degree relatives of melanoma patientsFirst-degree relatives of mutation carriersKin-cohort methodConfidence intervalsRisk of cancerMelanoma patientsLifetime riskProband's genotypeNon-melanomaFamily membersIncreased riskGastrointestinal cancerCDKN2A mutationsWilms tumorRiskMelanoma StudyPancreatic cancerNoncarriersGenotype distributionMelanoma
2024
Avocational exposure associations with ALS risk, survival, and phenotype: A Michigan-based case-control study
Goutman S, Boss J, Jang D, Piecuch C, Farid H, Batra M, Mukherjee B, Feldman E, Batterman S. Avocational exposure associations with ALS risk, survival, and phenotype: A Michigan-based case-control study. Journal Of The Neurological Sciences 2024, 457: 122899. PMID: 38278093, PMCID: PMC11060628, DOI: 10.1016/j.jns.2024.122899.Peer-Reviewed Original ResearchConceptsALS riskLower educational attainmentAssociated with ALS riskCase-control studyExercise 5Onset ageSelf-completionExposure variablesYard workExposure associationsRecreational danceIdentified exposureExerciseEducational attainmentAL burdenEnvironmental exposuresParticipantsAL factorPersonal participationAvocational exposureRiskExposomeHobbiesALS onsetComparison correction
2023
Uncovering associations between pre-existing conditions and COVID-19 Severity: A polygenic risk score approach across three large biobanks
Fritsche L, Nam K, Du J, Kundu R, Salvatore M, Shi X, Lee S, Burgess S, Mukherjee B. Uncovering associations between pre-existing conditions and COVID-19 Severity: A polygenic risk score approach across three large biobanks. PLOS Genetics 2023, 19: e1010907. PMID: 38113267, PMCID: PMC10763941, DOI: 10.1371/journal.pgen.1010907.Peer-Reviewed Original ResearchConceptsPolygenic risk scoresMichigan Genomics InitiativeUK BiobankPre-existing conditionsPhenome-wide association studyAssociation studiesCohort-specific analysesPolygenic risk score approachUK Biobank cohortMeta-analysisIncreased risk of hospitalizationGenome-wide association studiesBody mass indexRisk of hospitalizationIdentified novel associationsRisk score approachCOVID-19 outcome dataCOVID-19 hospitalizationCOVID-19Mass indexRisk scoreBiobankCardiovascular conditionsCOVID-19 severityIncreased riskEnvironmental risk scores of persistent organic pollutants associate with higher ALS risk and shorter survival in a new Michigan case/control cohort
Goutman S, Boss J, Jang D, Mukherjee B, Richardson R, Batterman S, Feldman E. Environmental risk scores of persistent organic pollutants associate with higher ALS risk and shorter survival in a new Michigan case/control cohort. Journal Of Neurology Neurosurgery & Psychiatry 2023, 95: 241-248. PMID: 37758454, PMCID: PMC11060633, DOI: 10.1136/jnnp-2023-332121.Peer-Reviewed Original ResearchConceptsEnvironmental risk scoreAmyotrophic lateral sclerosis riskPersistent organic pollutantsALS riskInterquartile increaseHigher ALS riskAssociated with ALS riskModify disease riskOrganochlorine pesticidesAssociated with riskRisk reduction strategiesPersistent organic pollutant analysisIndividual persistent organic pollutantsPersistent organic pollutant mixturesHazard ratioDisease riskRisk scoreCase/control cohortEnvironmental exposuresControl participantsGenetic susceptibilityPolychlorinated biphenylsAlpha-hexachlorocyclohexaneOrganic pollutantsMortality rateA framework for assessing interactions for risk stratification models: the example of ovarian cancer
Phung M, Lee A, McLean K, Anton-Culver H, Bandera E, Carney M, Chang-Claude J, Cramer D, Doherty J, Fortner R, Goodman M, Harris H, Jensen A, Modugno F, Moysich K, Pharoah P, Qin B, Terry K, Titus L, Webb P, Wu A, Zeinomar N, Ziogas A, Berchuck A, Cho K, Hanley G, Meza R, Mukherjee B, Pike M, Pearce C, Trabert B. A framework for assessing interactions for risk stratification models: the example of ovarian cancer. Journal Of The National Cancer Institute 2023, 115: 1420-1426. PMID: 37436712, PMCID: PMC10637032, DOI: 10.1093/jnci/djad137.Peer-Reviewed Original ResearchConceptsFamily history of ovarian cancerOvarian Cancer Association ConsortiumHistory of ovarian cancerFirst-degree family historyMenopausal statusRisk stratification modelCase-control studyRisk prediction modelOvarian cancerDisease riskAccurate risk stratification modelsStratification modelRisk/protective factorsDepot medroxyprogesterone acetate useProtective factorsFactor analysisRiskComprehensive analysis of interactionsCancerAcetate useUnequivocal riskStatusBreastfeedingAnalysis of interactionsPairwise interactionsCardiometabolic disease and obesity patterns differentially predict acute kidney injury after total joint replacement: a retrospective analysis
Leis A, Mathis M, Kheterpal S, Zawistowski M, Mukherjee B, Pace N, O'Reilly-Shah V, Smith J, Karvonen-Gutierrez C. Cardiometabolic disease and obesity patterns differentially predict acute kidney injury after total joint replacement: a retrospective analysis. British Journal Of Anaesthesia 2023, 131: 37-46. PMID: 37188560, PMCID: PMC10308436, DOI: 10.1016/j.bja.2023.04.001.Peer-Reviewed Original ResearchConceptsOdds of acute kidney injuryAcute kidney injuryCardiometabolic diseasesNon-Hispanic blacksGroup of hospitalsKidney injuryCardiometabolic patternTotal joint arthroplasty complicationsObesity statusObesity patternsIncreased oddsDisease co-occurrenceIncreased odds of AKIRetrospective analysisRisk of postoperative acute kidney injuryLatent class analysisLatent classesPostoperative acute kidney injuryRisk of acute kidney injuryRisk factorsDifferential riskTotal joint replacementMetabolic syndromeObesityPostoperative AKI risk
2022
The construction of cross-population polygenic risk scores using transfer learning
Zhao Z, Fritsche L, Smith J, Mukherjee B, Lee S. The construction of cross-population polygenic risk scores using transfer learning. American Journal Of Human Genetics 2022, 109: 1998-2008. PMID: 36240765, PMCID: PMC9674947, DOI: 10.1016/j.ajhg.2022.09.010.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesPolygenic risk scoresAncestry groupsTransferability of PRSPRS-CSPolygenic risk score methodsEuropean ancestry cohortsIndividuals of African ancestryIndividuals of South Asian ancestryNon-European ancestry groupsNon-European ancestrySouth Asian ancestryAssociation studiesDichotomous traitsSouth Asian sampleEuropean ancestryGenetic researchPRS modelAncestryAsian ancestryAfrican ancestryAfrican samplesUK BiobankRisk scoreAsian samplesOccupational history associates with ALS survival and onset segment
Goutman S, Boss J, Godwin C, Mukherjee B, Feldman E, Batterman S. Occupational history associates with ALS survival and onset segment. Amyotrophic Lateral Sclerosis And Frontotemporal Degeneration 2022, 24: 219-229. PMID: 36193557, PMCID: PMC10067530, DOI: 10.1080/21678421.2022.2127324.Peer-Reviewed Original ResearchConceptsStandard Occupational ClassificationOccupational settingsOnset segmentSelf-reported occupational exposureAmyotrophic Lateral Sclerosis RegistrySelf-reported exposureExposure to particulate matterCervical onsetStandard Occupational Classification codesMultinomial logistic regression modelCox proportional hazards modelsLogistic regression modelsSymptom onset to diagnosisOccupational pesticide exposureProportional hazards modelAssociated with workMaintenance occupationsGrounds cleaningALS clinicALS participantsProspective cohortAdjusted modelsDiagnosis ageAmyotrophic lateral sclerosis participantsOccupational historyExPRSweb: An online repository with polygenic risk scores for common health-related exposures
Ma Y, Patil S, Zhou X, Mukherjee B, Fritsche L. ExPRSweb: An online repository with polygenic risk scores for common health-related exposures. American Journal Of Human Genetics 2022, 109: 1742-1760. PMID: 36152628, PMCID: PMC9606385, DOI: 10.1016/j.ajhg.2022.09.001.Peer-Reviewed Original ResearchMeSH KeywordsGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansLipidsMultifactorial InheritanceRisk FactorsConceptsPolygenic risk scoresChronic conditionsPhenome-wide association studyMichigan Genomics InitiativeRisk scoreAssociation studiesHealth-related exposuresGenome-wide association studiesUK BiobankGenetic risk factorsPRS methodsFollow-up studyRisk factorsComplex traitsGenome InitiativeGenetic modifiersBiobankInfluence of exposureEnvironmental variablesScoresLipid levelsExpRLifestyleSmokingOnline repositoryAssociations of self-reported occupational exposures and settings to ALS: a case–control study
Goutman S, Boss J, Godwin C, Mukherjee B, Feldman E, Batterman S. Associations of self-reported occupational exposures and settings to ALS: a case–control study. International Archives Of Occupational And Environmental Health 2022, 95: 1567-1586. PMID: 35593931, PMCID: PMC9424174, DOI: 10.1007/s00420-022-01874-4.Peer-Reviewed Original ResearchConceptsStandard Occupational ClassificationStandard Occupational Classification codesExposure to particulate matterProductive occupationsALS riskSelf-reported occupational exposureHigher risk of amyotrophic lateral sclerosisOccupational exposureHigher ALS riskRisk of amyotrophic lateral sclerosisRisk factor modificationOccupational exposure to particulate matterExposure surveyIncreased ALS riskCase-control studyMaintenance occupationsGrounds cleaningFactor modificationExposure scoreTargeted screeningAmyotrophic lateral sclerosis diagnosisRepair occupationsAdaptive elastic net modelOccupational classificationProgressive neurological disease
2021
Maternal lipidomic signatures in relation to spontaneous preterm birth and large-for-gestational age neonates
Aung M, Ashrap P, Watkins D, Mukherjee B, Rosario Z, Vélez-Vega C, Alshawabkeh A, Cordero J, Meeker J. Maternal lipidomic signatures in relation to spontaneous preterm birth and large-for-gestational age neonates. Scientific Reports 2021, 11: 8115. PMID: 33854141, PMCID: PMC8046995, DOI: 10.1038/s41598-021-87472-9.Peer-Reviewed Original ResearchConceptsSpontaneous preterm birthBiomarkers of pregnancy outcomesGestational age neonatesPreterm birthAge neonatesPregnancy outcomesDegree of hydrocarbon chain saturationIncreased riskNeonatal anthropometric parametersAssociated with increased riskPlasmenyl phosphatidylethanolamineMaternal lipidomeWeeks gestationGestational ageLipidomic signatureAnthropometric parametersLiquid chromatography tandem mass spectrometryLipidomic profilesLipid metabolitesHydrocarbon chain saturationPlasma samplesBirthLogistic regressionHigh-performance liquid chromatography tandem mass spectrometryNeonatesExposure and risk factors for COVID-19 and the impact of staying home on Michigan residents
Wu K, Hornsby W, Klunder B, Krause A, Driscoll A, Kulka J, Bickett-Hickok R, Fellows A, Graham S, Kaleba E, Hayek S, Shi X, Sutton N, Douville N, Mukherjee B, Jamerson K, Brummett C, Willer C. Exposure and risk factors for COVID-19 and the impact of staying home on Michigan residents. PLOS ONE 2021, 16: e0246447. PMID: 33556117, PMCID: PMC7870003, DOI: 10.1371/journal.pone.0246447.Peer-Reviewed Original ResearchConceptsAfrican AmericansAnnual household income <Worsening health behaviorsLong-term health outcomesHousehold income <Low socioeconomic statusExposure to family membersHigher overall concernHigh riskExposure to familyHigh risk of contracting COVID-19Positive COVID-19 testLow-income groupsHealth behaviorsHealth outcomesRates of COVID-19 casesRental housingSocioeconomic statusClinical careRisk of contracting COVID-19COVID-19 preventionChronic diseasesInequality gapState of MichiganCOVID-19 cases
2020
Phenotype risk scores (PheRS) for pancreatic cancer using time-stamped electronic health record data: Discovery and validation in two large biobanks
Salvatore M, Beesley L, Fritsche L, Hanauer D, Shi X, Mondul A, Pearce C, Mukherjee B. Phenotype risk scores (PheRS) for pancreatic cancer using time-stamped electronic health record data: Discovery and validation in two large biobanks. Journal Of Biomedical Informatics 2020, 113: 103652. PMID: 33279681, PMCID: PMC7855433, DOI: 10.1016/j.jbi.2020.103652.Peer-Reviewed Original ResearchConceptsElectronic health recordsPolygenic risk scoresElectronic health record dataMichigan Genomics InitiativePhenotype risk scoreHigh-risk individualsPancreatic cancer diagnosisBody mass indexRisk scoreCancer diagnosisMedical phenomeUK Biobank (UKBHealth record dataSource of patient informationRisk predictionHypothesis-generating associationsDisease risk predictionHealth recordsUnadjusted associationsDrinking statusSmoking statusEpidemiological covariatesUKBPatient informationMultivariate associationsCancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks
Fritsche L, Patil S, Beesley L, VandeHaar P, Salvatore M, Ma Y, Peng R, Taliun D, Zhou X, Mukherjee B. Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks. American Journal Of Human Genetics 2020, 107: 815-836. PMID: 32991828, PMCID: PMC7675001, DOI: 10.1016/j.ajhg.2020.08.025.Peer-Reviewed Original ResearchConceptsPolygenic risk scoresGenome-wide association studiesMichigan Genomics InitiativeUK BiobankPopulation-based UK BiobankPolygenic risk score constructionPublished genome-wide association studiesLongitudinal biorepository effortAssociation studiesPredictive polygenic risk scoresRisk scoreNHGRI-EBI GWAS CatalogCancer traitsIndependent biobankMichigan MedicineGWAS CatalogGenome InitiativeBiobankScoresTraitsCancer researchOnline repositoryMichiganMedicineEvaluation
2019
Does Information on Blood Heavy Metals Improve Cardiovascular Mortality Prediction?
Wang X, Mukherjee B, Park S. Does Information on Blood Heavy Metals Improve Cardiovascular Mortality Prediction? Journal Of The American Heart Association 2019, 8: e013571. PMID: 31631727, PMCID: PMC6898859, DOI: 10.1161/jaha.119.013571.Peer-Reviewed Original ResearchConceptsCardiovascular diseaseNational Health and Nutrition Examination SurveyHealth and Nutrition Examination SurveyRisk factorsStudy sampleCardiovascular disease risk factorsCardiovascular disease mortalityCardiovascular disease risk assessmentImprove CVD risk predictionC-statisticNutrition Examination SurveyCardiovascular mortality predictionCVD risk predictionCox modelBlood markersExamination SurveyPrecision healthRisk scorePairwise interaction termsBlood metalsIntegrated discrimination improvementRisk predictionReclassification improvementMortality predictionInteraction termsExploring various polygenic risk scores for skin cancer in the phenomes of the Michigan genomics initiative and the UK Biobank with a visual catalog: PRSWeb
Fritsche L, Beesley L, VandeHaar P, Peng R, Salvatore M, Zawistowski M, Taliun S, Das S, LeFaive J, Kaleba E, Klumpner T, Moser S, Blanc V, Brummett C, Kheterpal S, Abecasis G, Gruber S, Mukherjee B. Exploring various polygenic risk scores for skin cancer in the phenomes of the Michigan genomics initiative and the UK Biobank with a visual catalog: PRSWeb. PLOS Genetics 2019, 15: e1008202. PMID: 31194742, PMCID: PMC6592565, DOI: 10.1371/journal.pgen.1008202.Peer-Reviewed Original ResearchConceptsMichigan Genomics InitiativeElectronic health recordsPolygenic risk scoresSkin cancer subtypesPheWAS resultsUK BiobankElectronic health record dataLongitudinal biorepository effortPhenome-wide association studyRisk scoreHealth record dataUK Biobank dataPrediction of disease riskPublicly-available sourcesHealth recordsGenetic architectureBiobank dataMichigan MedicineRecord dataSecondary phenotypesDisease riskVisual catalogAssociation studiesGenome InitiativePheWASAssociation Between Life Purpose and Mortality Among US Adults Older Than 50 Years
Alimujiang A, Wiensch A, Boss J, Fleischer N, Mondul A, McLean K, Mukherjee B, Pearce C. Association Between Life Purpose and Mortality Among US Adults Older Than 50 Years. JAMA Network Open 2019, 2: e194270. PMID: 31125099, PMCID: PMC6632139, DOI: 10.1001/jamanetworkopen.2019.4270.Peer-Reviewed Original ResearchConceptsHealth and Retirement StudyCause-specific mortalityAll-causeHealth outcomesUS adultsHealth and Retirement Study participantsCohort study of US adultsCause-specific mortality analysesInterview periodStudy of US adultsInfluence health outcomesAssociated with all-cause mortalityLife purposeCohort study sampleWeighted Cox proportional hazards modelsNational cohort studyPurpose in lifeQuality of lifeAll-cause mortalityCox proportional hazards modelsEnhance overall qualityAssociated with decreased mortalityProportional hazards modelRetirement StudyMortality associations