2024
Leveraging Functional Annotations Improves Cross-Population Genetic Risk Prediction
Ye Y, Xu L, Zhao H. Leveraging Functional Annotations Improves Cross-Population Genetic Risk Prediction. ICSA Book Series In Statistics 2024, 453-471. DOI: 10.1007/978-3-031-50690-1_18.Peer-Reviewed Original ResearchPolygenic risk scoresFunctional annotationGenetic risk predictionStandard PRSPost-GWAS analysisPolygenic risk score modelCross-population predictionNon-European populationsGenetic resultsGenetic studiesRisk predictionCross populationsAnnoPredPRS methodsUK BiobankAnnotationRisk scoreTraits/diseasesLDpredPopulationP+TPoor transferBiobankBayesian frameworkUsing clinical and genetic risk factors for risk prediction of 8 cancers in the UK Biobank
Hu J, Ye Y, Zhou G, Zhao H. Using clinical and genetic risk factors for risk prediction of 8 cancers in the UK Biobank. JNCI Cancer Spectrum 2024, 8: pkae008. PMID: 38366150, PMCID: PMC10919929, DOI: 10.1093/jncics/pkae008.Peer-Reviewed Original ResearchPolygenic risk scoresUK BiobankCancer riskClinical risk factorsRisk of breast cancerRisk factorsPolygenic risk score modelHigh risk of developing cancerRisk of developing cancerLate-onset patientsRisk predictionClinical variablesHigh-risk individualsCox proportional hazards modelsProportional hazards modelGenetic risk factorsBaseline traitsClinical risk modelRisk scoreEarly-onset patientsHazards modelLate-onset groupEarly-onset groupBreast cancerHigh risk
2023
Early breast cancer risk detection: a novel framework leveraging polygenic risk scores and machine learning
Tao L, Ye Y, Zhao H. Early breast cancer risk detection: a novel framework leveraging polygenic risk scores and machine learning. Journal Of Medical Genetics 2023, 60: 960-964. PMID: 37055164, DOI: 10.1136/jmg-2022-108582.Peer-Reviewed Original ResearchConceptsBreast cancerPolygenic risk scoresRisk scoreBC risk assessmentClinical breast examNon-genetic risk factorsHigh-risk individualsFemale participantsBreast examCancer deathCommon cancerBC screeningRisk factorsBC diagnosisDisease risk predictionDiagnostic stepsPopulation screeningGenetic riskRisk predictionUK BiobankCancerDiagnosisDiagnostic pipelineWomenDetection testA genome-wide association study of frailty identifies significant genetic correlation with neuropsychiatric, cardiovascular, and inflammation pathways
Ye Y, Noche R, Szejko N, Both C, Acosta J, Leasure A, Brown S, Sheth K, Gill T, Zhao H, Falcone G. A genome-wide association study of frailty identifies significant genetic correlation with neuropsychiatric, cardiovascular, and inflammation pathways. GeroScience 2023, 45: 2511-2523. PMID: 36928559, PMCID: PMC10651618, DOI: 10.1007/s11357-023-00771-z.Peer-Reviewed Original ResearchConceptsFried frailty scoreBiology of frailtyEuropean descent participantsOccurrence of frailtyGenome-wide association studiesMendelian randomization analysisFrailty scoreChronic painJoint disordersPolygenic risk scoresRespiratory diseaseInflammation pathwaysRisk scoreClinical phenotypeBrain tissueCausal associationFrailtyAge-related pathwaysRandomization analysisGenetic factorsAssociation studiesUK BiobankRetirement StudyPerson's vulnerabilitySignificant genetic correlations
2022
Glaucoma Genetic Risk Scores in the Million Veteran Program
Waksmunski A, Kinzy T, Cruz L, Nealon C, Halladay C, Simpson P, Canania R, Anthony S, Roncone D, Rogers L, Leber J, Dougherty J, Greenberg P, Sullivan J, Wu W, Iyengar S, Crawford D, Peachey N, Bailey J, Gaziano J, Ramoni R, Breeling J, Chang K, Huang G, Muralidhar S, O’Donnell C, Tsao P, Muralidhar S, Moser J, Whitbourne S, Brewer J, Concato J, Warren S, Argyres D, Tsao P, Stephens B, Brophy M, Humphries D, Do N, Shayan S, Nguyen X, O’Donnell C, Pyarajan S, Cho K, Pyarajan S, Hauser E, Sun Y, Zhao H, Wilson P, McArdle R, Dellitalia L, Harley J, Whittle J, Beckham J, Wells J, Gutierrez S, Gibson G, Kaminsky L, Villareal G, Kinlay S, Xu J, Hamner M, Haddock K, Bhushan S, Iruvanti P, Godschalk M, Ballas Z, Buford M, Mastorides S, Klein J, Ratcliffe N, Florez H, Swann A, Murdoch M, Sriram P, Yeh S, Washburn R, Jhala D, Aguayo S, Cohen D, Sharma S, Callaghan J, Oursler K, Whooley M, Ahuja S, Gutierrez A, Schifman R, Greco J, Rauchman M, Servatius R, Oehlert M, Wallbom A, Fernando R, Morgan T, Stapley T, Sherman S, Anderson G, Tsao P, Sonel E, Boyko E, Meyer L, Gupta S, Fayad J, Hung A, Lichy J, Hurley R, Robey B, Striker R. Glaucoma Genetic Risk Scores in the Million Veteran Program. Ophthalmology 2022, 129: 1263-1274. PMID: 35718050, PMCID: PMC9997524, DOI: 10.1016/j.ophtha.2022.06.012.Peer-Reviewed Original ResearchConceptsPrimary open-angle glaucomaInvasive glaucoma surgeryRisk stratificationMillion Veteran ProgramEffect estimatesPOAG casesEuropean ancestryOpen-angle glaucomaCross-sectional studyDegenerative eye diseasesAfrican ancestryVeteran ProgramGenetic risk scoreAggressive treatmentGlaucoma surgeryEarly treatmentIrreversible blindnessEye diseaseHigh riskRisk scoreIncremental riskVisual impairmentGenetic riskVeteransRisk variants
2021
Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-Treatment DNA Methylation in Peripheral Blood
Qian D, Ulrich B, Peng G, Zhao H, Conneely K, Miller A, Bruner D, Eldridge R, Wommack E, Higgins K, Shin D, Saba N, Smith A, Burtness B, Park H, Stokes W, Beitler J, Xiao C. Outcomes Stratification of Head and Neck Cancer Using Pre- and Post-Treatment DNA Methylation in Peripheral Blood. International Journal Of Radiation Oncology • Biology • Physics 2021, 111: s143-s144. DOI: 10.1016/j.ijrobp.2021.07.323.Peer-Reviewed Original ResearchProgression-free survivalSquamous cell carcinomaOverall survivalHigh-risk scoreRisk scoreDiscovery cohortValidation cohortPeripheral bloodRisk factorsNon-metastatic squamous cell carcinomaMethods Peripheral blood samplesWorse progression-free survivalShorter progression-free survivalPoor progression-free survivalNeck squamous cell carcinomaHPV-negative statusPEG tube insertionPost-treatment time pointsCompletion of radiotherapyHigher neutrophil countOral cavity cancerNeck cancer recurrenceAforementioned risk factorsPeripheral blood samplesClinicopathologic covariatesPsychological trauma and the genetic overlap between posttraumatic stress disorder and major depressive disorder
Mundy J, Hübel C, Gelernter J, Levey D, Murray RM, Skelton M, Stein MB, Maihofer A, Nievergelt C, Baker D, Risborough V, Calabrese J, Galea S, Stein D, Koen N, Dalvie S, Aiello A, Roberts A, Koenen K, Solovieff N, Kranzler H, Zhao H, Gelernter J, Farrer L, Johnson E, Rice J, Bierut L, Saccone N, McFarlane A, Forbes D, Silove D, O'Donnell M, Bryant R, van Hooff M, Sponheim S, Disner S, Pietrzak R, Chen C, Smoller J, Stein M, Ursano R, Kessler R, Junglen A, Delahanty D, Amstadter A, Sheerin C, Ruggiero K, McLaughlin K, Peverill M, Caldas-de-Almeida J, Austin S, Gelaye B, Williams M, Sanchez S, Franz C, Panizzon M, Lyons M, Kremen W, Andreassen O, Dale A, Rutten B, Vinkers C, Schijven D, Geuze E, Vermetten E, Luykx J, Boks M, Ashley-Koch A, Beckham J, Garrett M, Hauser M, Dennis M, Kimbrel N, Qin X, Karstoft K, Andersen S, Borglum A, Hougaard D, Bybjerg-Grauholm J, Duncan L, Bµkvad-Hansen M, Nordentoft M, Mors O, Mortensen P, Werge T, Thompson W, Wang Y, Heath A, Nelson E, Martin N, Gordon S, Wolf E, Logue M, Miller M, McGlinchey R, Milberg W, Erbes C, Polusny M, Arbisi P, Peterson A, Williamson D, Young K, Maurer D, Rothbaum A, Zoellner L, Mavissakalian M, Feeny N, Roy-Byrne P, Rothbaum B, Maples-Keller J, Khan A, Wolff J, Lebois L, Teicher M, Kaufman M, Winternitz S, Bolger E, Seligowski A, Orcutt H, Evans A, Lugonja B, Lewis C, Jones I, Bisson J, McLean S, Linnstaedt S, Peters E, Rung A, Trapido E, Brashear M, Lori A, Smith A, Bradley B, Gillespie C, Guffanti G, Ressler K, Almli L, Jovanovic T, Bustamante A, Uddin M, van den Heuvel L, Seedat S, Hemmings S, Uka A, Kulenovic A, Wolf C, Babic D, Avdibegovic E, Deckert J, Domschke K, Jakovljevic M, Marmar C, Flory J, Jett M, Yehuda R, Hammamieh R, King A, Liberzon I, Seng J, Morris C, Mehta D, Voisey J, Lawford B, Young R, McLeay S, Daskalakis N, Norman S, Wang Z, Breen G, Coleman J, Klengel T, Torres K, Choi K, Levey D, Polimanti R, Atkinson E, Martin A, Neale B, Daly M, Ripke S, Ratanatharathorn A, Provost A, Haas M, Stevens J, Morey R, Harnal S, Mortensen P, Seedat S, Sumner J, Vassos E, Breen G, Coleman J. Psychological trauma and the genetic overlap between posttraumatic stress disorder and major depressive disorder. Psychological Medicine 2021, 52: 3975-3984. PMID: 34085609, PMCID: PMC8962503, DOI: 10.1017/s0033291721000830.Peer-Reviewed Original ResearchRecurrent major depressive disorderMajor depressive disorderPosttraumatic stress disorderSingle-episode major depressive disorderDepressive disorderTrauma exposureStress disorderPsychological trauma exposureLifetime major depressive disorderTrauma sensitivityGenetic loadingUK Biobank participantsKey risk factorsMental health consequencesRisk factorsMillion Veteran ProgramPolygenic risk scoresRisk scoreGenetic overlapHealth consequencesBiobank participantsTraumaDisordersVeteran ProgramPsychiatric Genomics ConsortiumInteractions Between Enhanced Polygenic Risk Scores and Lifestyle for Cardiovascular Disease, Diabetes, and Lipid Levels
Ye Y, Chen X, Han J, Jiang W, Natarajan P, Zhao H. Interactions Between Enhanced Polygenic Risk Scores and Lifestyle for Cardiovascular Disease, Diabetes, and Lipid Levels. Circulation Genomic And Precision Medicine 2021, 14: e003128. PMID: 33433237, PMCID: PMC7887077, DOI: 10.1161/circgen.120.003128.Peer-Reviewed Original ResearchConceptsType 2 diabetesAbsolute risk reductionPolygenic risk scoresLifestyle adherenceCardiovascular diseaseGenetic riskRisk scoreCoronary artery diseaseBody mass indexGreater absolute benefitHigher polygenic risk scoreHigh genetic riskAdditive interactionRisk reductionArtery diseaseLDL cholesterolTotal cholesterolAtrial fibrillationMass indexAbsolute benefitTriglyceride levelsRisk factorsLipid levelsPhysical activityLifestyle status
2020
Genetic Architecture of Abdominal Aortic Aneurysm in the Million Veteran Program
Klarin D, Verma S, Judy R, Dikilitas O, Wolford B, Paranjpe I, Levin M, Pan C, Tcheandjieu C, Spin J, Lynch J, Assimes T, Åldstedt Nyrønning L, Mattsson E, Edwards T, Denny J, Larson E, Lee M, Carrell D, Zhang Y, Jarvik G, Gharavi A, Harley J, Mentch F, Pacheco J, Hakonarson H, Skogholt A, Thomas L, Gabrielsen M, Hveem K, Nielsen J, Zhou W, Fritsche L, Huang J, Natarajan P, Sun Y, DuVall S, Rader D, Cho K, Chang K, Wilson P, O’Donnell C, Kathiresan S, Scali S, Berceli S, Willer C, Jones G, Bown M, Nadkarni G, Kullo I, Ritchie M, Damrauer S, Tsao P, Gaziano J, Ramoni R, Beckham J, Breeling J, Chang K, Huang G, Muralidhar S, O’Donnell C, Casas Romero J, Tsao P, Muralidhar S, Moser J, Whitbourne S, Brewer J, Concato J, Warren S, Argyres D, Tsao P, Gaziano J, Stephens B, Brophy M, Humphries D, Do N, Shayan S, Nguyen X, O’Donnell C, Pyarajan S, Tsao P, Cho K, Pyarajan S, Hauser E, Sun Y, Zhao H, Wilson P, McArdle R, Dellitalia L, Harley J, Zablocki C, Whittle J, Beckham J, Wells J, Gutierrez S, Gibson G, Kaminsky L, Villareal G, Kinlay S, Xu J, Hamner M, Haddock K, Bhushan S, Iruvanti P, Godschalk M, Ballas Z, Buford M, Mastorides S, Klein J, Ratcliffe N, Florez H, Swann A, Murdoch M, Sriram P, Yeh S, Washburn R, Jhala D, Aguayo S, Cohen D, Sharma S, Callaghan J, Oursler K, Whooley M, Ahuja S, Gutierrez A, Schifman R, Greco J, Rauchman M, Servatius R, Oehlert M, Wallbom A, Fernando R, Morgan T, Stapley T, Sherman S, Anderson G, Tsao P, Sonel E, Boyko E, Meyer L, Gupta S, Fayad J, Hung A, Lichy J, Hurley R, Robey B, Striker R. Genetic Architecture of Abdominal Aortic Aneurysm in the Million Veteran Program. Circulation 2020, 142: 1633-1646. PMID: 32981348, PMCID: PMC7580856, DOI: 10.1161/circulationaha.120.047544.Peer-Reviewed Original ResearchConceptsAbdominal aortic aneurysmBlood pressurePolygenic risk scoresAortic aneurysmFamily historyDiastolic blood pressureSystolic blood pressureGenome-wide polygenic risk scoreRisk variantsSmoking risk factorsMendelian randomization analysisAAA prevalenceCardiovascular mortalityRisk factorsAAA developmentArterial bedCurrent guidelinesVascular territoriesLower extremitiesMillion Veteran ProgramRisk scoreTherapeutic implicationsCurrent screeningImportant causeAAA risk
2017
T45 Genetic Factor Common To Schizophrenia And Hiv Infection Is Associated With Risky Sexual Behavior
Wang Q, Polimanti R, Kranzler H, Farrer L, Zhao H, Gelernter J. T45 Genetic Factor Common To Schizophrenia And Hiv Infection Is Associated With Risky Sexual Behavior. European Neuropsychopharmacology 2017, 27: s460-s461. DOI: 10.1016/j.euroneuro.2016.09.533.Peer-Reviewed Original ResearchRisky sexual behaviorBody mass indexHIV infectionPolygenic risk scoresRisk scoreSexual behaviorHuman immunodeficiency virus (HIV) infectionSame effect directionImmunodeficiency virus infectionSZ-polygenic risk scoreGenetic risk factorsGenetic risk scoreSemi-Structured AssessmentMass indexRisk factorsEpidemiologic correlationsVirus infectionObservational studySynaptic transmissionHIVBipolar disorderNerve impulse transmissionSerious disorderDrug dependenceInfection