2023
Family and personal history of cancer in the All of Us research program for precision medicine
Bruce L, Paul P, Kim K, Kim J, Keegan T, Hiatt R, Ohno-Machado L, Investigators O. Family and personal history of cancer in the All of Us research program for precision medicine. PLOS ONE 2023, 18: e0288496. PMID: 37459328, PMCID: PMC10351738, DOI: 10.1371/journal.pone.0288496.Peer-Reviewed Original ResearchCommon and rare variants associated with cardiometabolic traits across 98,622 whole-genome sequences in the All of Us research program
Wang X, Ryu J, Kim J, Ramirez A, Mayo K, Condon H, Vaitinadin N, Ohno-Machado L, Talavera G, Ellinor P, Lubitz S, Choi S. Common and rare variants associated with cardiometabolic traits across 98,622 whole-genome sequences in the All of Us research program. Journal Of Human Genetics 2023, 68: 565-570. PMID: 37072623, PMCID: PMC10524735, DOI: 10.1038/s10038-023-01147-z.Peer-Reviewed Original ResearchConceptsDiverse human populationsGenomic dataGene-based burden testsWhole genome sequencesRare variant analysisHuman populationQuantitative traitsBurden testsRare lossLociComplex diseasesGenetic associationVariant analysisFunction variantsCardiometabolic traitsRare variantsTraitsBiomedical researchGIGYF1VariantsNPR2ACANSequencePopulationLDLRBlockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions
Kuo T, Pham A, Edelson M, Kim J, Chan J, Gupta Y, Ohno-Machado L, Anderson D, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bell D, Bernstam E, Ngan C, Day M, Doctor J, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hinske L, Hu Z, Ir D, Jiang X, Kim K, Kim J, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Matheny M, Meeker D, Mou Z, Neumann L, Nguyen N, Nick A, Ohno-Machado L, Park E, Paul P, Pletcher M, Post K, Rieder C, Scherer C, Schilling L, Soares A, SooHoo S, Soysal E, Steven C, Tep B, Toy B, Wang B, Wu Z, Xu H, Yong C, Zheng K, Zhou Y, Zucker R. Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions. Journal Of The American Medical Informatics Association 2023, 30: 1167-1178. PMID: 36916740, PMCID: PMC10198529, DOI: 10.1093/jamia/ocad049.Peer-Reviewed Original ResearchConceptsFederated data analysisUser activity logsSmart contract deploymentRun-time efficiencyData analysis systemData analysis activitiesActivity logsData discoveryQuerying timeBlockchain systemBlockchain technologyNetwork transactionsCOVID-19 data analysisMultiple institutionsLow deploymentBlockchainGitHub repositoryMultiple nodesLarge networksQueriesAnalysis activitiesHigh availabilityLanguage codeBaseline solutionData analysis
2022
Comparative Safety and Effectiveness of Biologic Therapy for Crohn’s Disease: A CA-IBD Cohort Study
Singh S, Kim J, Luo J, Paul P, Rudrapatna V, Park S, Zheng K, Syal G, Ha C, Fleshner P, McGovern D, Sauk J, Limketkai B, Dulai P, Boland B, Eisenstein S, Ramamoorthy S, Melmed G, Mahadevan U, Sandborn W, Ohno-Machado L. Comparative Safety and Effectiveness of Biologic Therapy for Crohn’s Disease: A CA-IBD Cohort Study. Clinical Gastroenterology And Hepatology 2022, 21: 2359-2369.e5. PMID: 36343846, PMCID: PMC12145724, DOI: 10.1016/j.cgh.2022.10.029.Peer-Reviewed Original ResearchConceptsTNF-α antagonistsRisk of hospitalizationUstekinumab-treated patientsCrohn's diseaseSerious infectionsLower riskMulticenter cohortInflammatory bowel disease-related surgeryTumor necrosis factor α antagonistsNecrosis factor α antagonistsDisease-related surgeryHigher comorbidity burdenVedolizumab-treated patientsNew biologic agentsPropensity-score matchingComorbidity burdenCause hospitalizationAdult patientsBiologic therapyCohort studyPrior hospitalizationBiologic agentsΑ antagonistsBiologic classesComparative safetyThe evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition
Kuo T, Jiang X, Tang H, Wang X, Harmanci A, Kim M, Post K, Bu D, Bath T, Kim J, Liu W, Chen H, Ohno-Machado L. The evolving privacy and security concerns for genomic data analysis and sharing as observed from the iDASH competition. Journal Of The American Medical Informatics Association 2022, 29: 2182-2190. PMID: 36164820, PMCID: PMC9667175, DOI: 10.1093/jamia/ocac165.Peer-Reviewed Original ResearchConceptsSensitive personal informationGenomic data analysisPotential future research directionsPersonal informationSecurity concernsGenomics data repositoryData repositoryReport lessonsProtection techniquesFuture research directionsPrivacyResearch directionsData usePractical challengesGenomic dataData analysisAnonymizationCommunity effortsRepositorySecurityBiomedical researchInformationDataChallengesEthnic and Racial Inequities in Cancer Screening During the COVID-19 Pandemic: a multi-site observational study in the United States
Idossa D, Borno H, Wang K, Pletcher M, Gresham G, Canchola A, Bell D, Matheny M, Schilling L, Perkins A, Zheng K, Ohno-Machado L, Kim J, Soohoo S, Meeker D, Gomez S. Ethnic and Racial Inequities in Cancer Screening During the COVID-19 Pandemic: a multi-site observational study in the United States. International Journal Of Cancer Care And Delivery 2022, 2 DOI: 10.53876/001c.37412.Peer-Reviewed Original ResearchCancer screeningBlack individualsProstate cancer screeningSARS-CoV2 infectionColon cancer screeningMulti-site observational studyCOVID-19 pandemicRelative reductionSurgical resectionProstate resectionProstate cancerCurrent COVID-19 pandemicObservational studyColon cancerSARS-CoV2Largest relative declineLargest relative reductionInfection rateDiagnostic mammogramsDiagnostic proceduresScreening activitiesBreastStudy periodDiagnostic mammographyColonEffect of Obesity on Risk of Hospitalization, Surgery, and Serious Infection in Biologic-Treated Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study
Gu P, Luo J, Kim J, Paul P, Limketkai B, Sauk J, Park S, Parekh N, Zheng K, Rudrapatna V, Syal G, Ha C, McGovern D, Melmed G, Fleshner P, Eisenstein S, Ramamoorthy S, Dulai P, Boland B, Grunvald E, Mahadevan U, Ohno-Machado L, Sandborn W, Singh S. Effect of Obesity on Risk of Hospitalization, Surgery, and Serious Infection in Biologic-Treated Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. The American Journal Of Gastroenterology 2022, 117: 1639-1647. PMID: 35973139, DOI: 10.14309/ajg.0000000000001855.Peer-Reviewed Original ResearchConceptsInflammatory bowel diseaseBiologic-treated patientsRisk of hospitalizationBody mass indexNormal body mass indexSerious infectionsBiologic agentsBowel diseaseCox proportional hazards analysisWorld Health Organization classificationEffect of obesityProportional hazards analysisElectronic health recordsCause hospitalizationVisceral obesityAdult patientsBaseline demographicsBiologic initiationBiologic therapyCohort studyEndoscopic outcomesMass indexOrganization classificationTreatment characteristicsStratified analysisEffectiveness and Safety of Biologic Therapy in Hispanic Vs Non-Hispanic Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study
Nguyen N, Luo J, Paul P, Kim J, Syal G, Ha C, Rudrapatna V, Park S, Parekh N, Zheng K, Sauk J, Limketkai B, Fleshner P, Eisenstein S, Ramamoorthy S, Melmed G, Dulai P, Boland B, Mahadevan U, Sandborn W, Ohno-Machado L, McGovern D, Singh S. Effectiveness and Safety of Biologic Therapy in Hispanic Vs Non-Hispanic Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. Clinical Gastroenterology And Hepatology 2022, 21: 173-181.e5. PMID: 35644340, PMCID: PMC9701245, DOI: 10.1016/j.cgh.2022.05.008.Peer-Reviewed Original ResearchConceptsInflammatory bowel diseaseNon-Hispanic patientsBiologic-treated patientsHispanic patientsSerious infectionsBiologic therapyBowel diseasePropensity score-matched cohortBurden of inflammationRisk of hospitalizationHigh ratePropensity-score matchingCause hospitalizationAdult patientsBiologic initiationCohort studyBiologic agentsMedication useHigh burdenHigh riskHospitalizationPatientsSurvival analysisSurgeryAbstractTextSu1018: UNPLANNED HEALTHCARE UTILIZATION AND SAFETY OF BIOLOGIC THERAPY IN HISPANIC VS. NON-HISPANIC PATIENTS WITH IBD
Nguyen N, Luo J, Paul P, Kim J, Syal G, Ha C, Rudrapatna V, Park S, Parekh N, Zheng K, Sauk J, Limketkai B, Fleshner P, Eisenstein S, Ramamoorthy S, Melmed G, Boland B, Mahadevan U, Sandborn W, Ohno-Machado L, Mcgovern D, Singh S. Su1018: UNPLANNED HEALTHCARE UTILIZATION AND SAFETY OF BIOLOGIC THERAPY IN HISPANIC VS. NON-HISPANIC PATIENTS WITH IBD. Gastroenterology 2022, 162: s-482-s-483. DOI: 10.1016/s0016-5085(22)61145-4.Peer-Reviewed Original ResearchProtein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis
Povero D, Tameda M, Eguchi A, Ren W, Kim J, Myers R, Goodman Z, Harrison S, Sanyal A, Bosch J, Ohno-Machado L, Feldstein A. Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis. Scientific Reports 2022, 12: 3027. PMID: 35194091, PMCID: PMC8863778, DOI: 10.1038/s41598-022-06809-0.Peer-Reviewed Original ResearchConceptsSmall non-coding RNAsExtracellular vesiclesNon-coding RNAsNovel miRNAsControl subjectsFurther molecular characterizationMiRNA sequence analysisLiver-specific markersProtein profilingMiRNA cargoMolecular characterizationHuman diseasesCurrent serum markersNovel surrogate biomarkersPrimary sclerosing cholangitisCholestatic liver diseaseHealthy control subjectsMiRNA profilesProteinCell specificityDifferential centrifugationMiRNAsPSC patientsSclerosing cholangitisLiver disease
2021
Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track
Kuo T, Bath T, Ma S, Pattengale N, Yang M, Cao Y, Hudson C, Kim J, Post K, Xiong L, Ohno-Machado L. Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track. International Journal Of Medical Informatics 2021, 154: 104559. PMID: 34474309, PMCID: PMC9933142, DOI: 10.1016/j.ijmedinf.2021.104559.Peer-Reviewed Original ResearchConceptsSecure genome analysis competitionData retrieval queriesBlockchain-based methodData sharing methodReal-world problemsQuery indexType of sharingRetrieval queriesBlockchain technologyLedger technologySource codeBlockchain utilizationBlockchain strategyHealthcare applicationsInteraction recordsSharing methodTest datasetSharing recordsBiomedical research applicationsConsortium resourcesNew platformPatient recordsBlockchainQueriesTechnologyPrivacy-protecting, reliable response data discovery using COVID-19 patient observations
Kim J, Neumann L, Paul P, Day M, Aratow M, Bell D, Doctor J, Hinske L, Jiang X, Kim K, Matheny M, Meeker D, Pletcher M, Schilling L, SooHoo S, Xu H, Zheng K, Ohno-Machado L, Anderson D, Anderson N, Balacha C, Bath T, Baxter S, Becker-Pennrich A, Bernstam E, Carter W, Chau N, Choi Y, Covington S, DuVall S, El-Kareh R, Florian R, Follett R, Geisler B, Ghigi A, Gottlieb A, Hu Z, Ir D, Knight T, Koola J, Kuo T, Lee N, Mansmann U, Mou Z, Murphy R, Neumann L, Nguyen N, Niedermayer S, Park E, Perkins A, Post K, Rieder C, Scherer C, Soares A, Soysal E, Tep B, Toy B, Wang B, Wu Z, Zhou Y, Zucker R. Privacy-protecting, reliable response data discovery using COVID-19 patient observations. Journal Of The American Medical Informatics Association 2021, 28: 1765-1776. PMID: 34051088, PMCID: PMC8194878, DOI: 10.1093/jamia/ocab054.Peer-Reviewed Original ResearchVERTIcal Grid lOgistic regression with Confidence Intervals (VERTIGO-CI).
Kim J, Li W, Bath T, Jiang X, Ohno-Machado L. VERTIcal Grid lOgistic regression with Confidence Intervals (VERTIGO-CI). AMIA Joint Summits On Translational Science Proceedings 2021, 2021: 355-364. PMID: 34457150, PMCID: PMC8378611.Peer-Reviewed Original ResearchConceptsDual spaceCovariance matrixVariance estimationSpace modelTest statisticKernel matrixLinear modelReal dataTolerable performanceNovel extensionDual-space modelPoint estimatesEquivalent accuracyCentralized versionStatisticsRegression modelsModelMatrixExtensionDual objectivesCentralized settingFederated LearningEstimationPrivacy-preserving mannerSpacePredictive Analytics for Glaucoma Using Data From the All of Us Research Program
Baxter S, Saseendrakumar B, Paul P, Kim J, Bonomi L, Kuo T, Loperena R, Ratsimbazafy F, Boerwinkle E, Cicek M, Clark C, Cohn E, Gebo K, Mayo K, Mockrin S, Schully S, Ramirez A, Ohno-Machado L, Investigators A. Predictive Analytics for Glaucoma Using Data From the All of Us Research Program. American Journal Of Ophthalmology 2021, 227: 74-86. PMID: 33497675, PMCID: PMC8184631, DOI: 10.1016/j.ajo.2021.01.008.Peer-Reviewed Original ResearchConceptsGlaucoma surgeryPrimary open-angle glaucomaOphthalmic researchSingle-center cohortElectronic health record dataMultivariable logistic regressionSingle-center dataOpen-angle glaucomaHealth record dataMean ageClaims dataUs Research ProgramLogistic regressionSurgeryRecord dataOphthalmic imagingCharacteristic curveExternal validationGlaucomaCohortAUCSingle-center model
2020
Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis mice
Eguchi A, Yan R, Pan S, Wu R, Kim J, Chen Y, Ansong C, Smith R, Tempaku M, Ohno-Machado L, Takei Y, Feldstein A, Tsukamoto H. Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1β and IL-17 upregulation in alcoholic hepatitis mice. Journal Of Molecular Medicine 2020, 98: 1021-1034. PMID: 32556367, PMCID: PMC7810220, DOI: 10.1007/s00109-020-01926-7.Peer-Reviewed Original ResearchConceptsHepatic stellate cellsAlcoholic liver diseaseAlcoholic hepatitisAH miceIL-1βHepatic macrophagesStellate cellsExtracellular vesiclesPrimary hepatic stellate cellsIL-17 upregulationIL-17 productionUpregulated IL-1βHepatocyte-derived extracellular vesiclesNovel murine modelTLR9-dependent mannerMacrophage IL-1βHepatitis miceIL-17Liver diseaseControl miceCytokine productionLiver pathologyLiver fibrogenesisMurine modelΑ-SMA
2019
Patient Perspectives About Decisions to Share Medical Data and Biospecimens for Research
Kim J, Kim H, Bell E, Bath T, Paul P, Pham A, Jiang X, Zheng K, Ohno-Machado L. Patient Perspectives About Decisions to Share Medical Data and Biospecimens for Research. JAMA Network Open 2019, 2: e199550. PMID: 31433479, PMCID: PMC6707015, DOI: 10.1001/jamanetworkopen.2019.9550.Peer-Reviewed Original ResearchEvaluating and sharing global genetic ancestry in biomedical datasets
Harismendy O, Kim J, Xu X, Ohno-Machado L. Evaluating and sharing global genetic ancestry in biomedical datasets. Journal Of The American Medical Informatics Association 2019, 26: 457-461. PMID: 30869786, PMCID: PMC6433181, DOI: 10.1093/jamia/ocy194.Peer-Reviewed Original ResearchConceptsGenetic diversity measurementsGenetic ancestryAvailable molecular datasetsHuman genetics researchCancer Genome Atlas (TCGA) datasetContinental resolutionGenetic diversityPhenotype-genotype associationsMolecular datasetsGlobal genetic ancestryAncestry informationGenetic researchAtlas datasetDiversity measurementsAncestryTraitsGlobal scaleDiversityBiomedical datasetsAvailable datasetsData repositoryDisease riskAccess datasetDatasetAvailable cohorts
2018
Genomics and electronic health record systems
Ohno-Machado L, Kim J, Gabriel R, Kuo G, Hogarth M. Genomics and electronic health record systems. Human Molecular Genetics 2018, 27: r48-r55. PMID: 29741693, PMCID: PMC5946823, DOI: 10.1093/hmg/ddy104.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsElectronic health recordsHigh-level viewElectronic health record systemsHealth record systemsNext generation systemsEHR systemsSeamless fashionOpen issuesMyriad of approachesHealth recordsRecord systemSpecific solutionsEnd goalSources of informationAnalysis of genomesInformationCustomizationSystemGeneration systemVisionDegrees of successFunctionality
2017
Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies
Wang M, Ji Z, Wang S, Kim J, Yang H, Jiang X, Ohno-Machado L. Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies. Bioinformatics 2017, 33: 3716-3725. PMID: 29036461, PMCID: PMC5860319, DOI: 10.1093/bioinformatics/btx470.Peer-Reviewed Original ResearchA Predictive Model for Extended Postanesthesia Care Unit Length of Stay in Outpatient Surgeries
Gabriel R, Waterman R, Kim J, Ohno-Machado L. A Predictive Model for Extended Postanesthesia Care Unit Length of Stay in Outpatient Surgeries. Anesthesia & Analgesia 2017, 124: 1529-1536. PMID: 28079580, DOI: 10.1213/ane.0000000000001827.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAge FactorsAgedAged, 80 and overAmbulatory Surgical ProceduresAnesthesiaChildChild, PreschoolCritical CareFemaleForecastingHumansHypertensionInfantInfant, NewbornIntensive Care UnitsLength of StayLogistic ModelsMaleMiddle AgedModels, StatisticalObesity, MorbidPostoperative CareRisk FactorsROC CurveYoung AdultConceptsPACU lengthPostanesthesia care unit lengthPrimary anesthesia typePostanesthesia care unitHosmer-Lemeshow testLogistic regression modelsAnesthesia typeMorbid obesityCare unitHL testOutpatient surgeryOutpatient procedureSingle institutionHigher oddsNonsignificant P valuesStayPatientsSurgical specialtiesROC curveGood calibrationCharacteristic curveExcellent discriminationAUC valuesP-valueBackward elimination
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