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
2020
Cancer 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 repositoryMichiganMedicineEvaluationExpanding Our Understanding of Ovarian Cancer Risk: The Role of Incomplete Pregnancies
Lee AW, Rosenzweig S, Wiensch A, Group T, Ramus SJ, Menon U, Gentry-Maharaj A, Ziogas A, Anton-Culver H, Whittemore AS, Sieh W, Rothstein JH, McGuire V, Wentzensen N, Bandera EV, Qin B, Terry KL, Cramer DW, Titus L, Schildkraut JM, Berchuck A, Goode EL, Kjaer SK, Jensen A, Jordan SJ, Ness RB, Modugno F, Moysich K, Thompson PJ, Goodman MT, Carney ME, Chang-Claude J, Rossing MA, Harris HR, Doherty JA, Risch HA, Khoja L, Alimujiang A, Phung MT, Brieger K, Mukherjee B, Pharoah PDP, Wu AH, Pike MC, Webb PM, Pearce CL. Expanding Our Understanding of Ovarian Cancer Risk: The Role of Incomplete Pregnancies. Journal Of The National Cancer Institute 2020, 113: 301-308. PMID: 32766851, PMCID: PMC7936053, DOI: 10.1093/jnci/djaa099.Peer-Reviewed Original ResearchConceptsOvarian cancer riskInvasive epithelial ovarian cancerClear cell ovarian cancerIncomplete pregnanciesEpithelial ovarian cancerOvarian cancerOvarian Cancer Association ConsortiumCancer riskOdds ratioInvasive epithelial ovarian cancer casesEpithelial ovarian cancer casesHistotype-specific analysesHistotype-specific associationsOral contraceptive useInvasive ovarian cancerHistory of breastfeedingConfidence intervalsOvarian cancer casesCase-control studyOCAC studiesMajor histotypesPooled analysisInverse associationCancer casesComplete pregnancyA Fast and Accurate Method for Genome-Wide Time-to-Event Data Analysis and Its Application to UK Biobank
Bi W, Fritsche L, Mukherjee B, Kim S, Lee S. A Fast and Accurate Method for Genome-Wide Time-to-Event Data Analysis and Its Application to UK Biobank. American Journal Of Human Genetics 2020, 107: 222-233. PMID: 32589924, PMCID: PMC7413891, DOI: 10.1016/j.ajhg.2020.06.003.Peer-Reviewed Original ResearchConceptsControlled type I error ratesTime-to-event data analysisType I error rateGenetic studies of human diseasesGenome-wide significance levelTime-to-event phenotypesSaddlepoint approximationGenome-wide analysisEuropean ancestry samplesMinor allele frequencyStudy of human diseaseElectronic health recordsCox PH regression modelRegression modelsStandard Wald testProportional hazardsBinary phenotypesData analysisAncestry samplesGenetic studiesHealth recordsUK BiobankAllele frequenciesInpatient dataCox proportional hazards
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 testExploring 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 InitiativePheWAS