2020
Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers
Zhang YD, Hurson AN, Zhang H, Choudhury PP, Easton DF, Milne RL, Simard J, Hall P, Michailidou K, Dennis J, Schmidt MK, Chang-Claude J, Gharahkhani P, Whiteman D, Campbell PT, Hoffmeister M, Jenkins M, Peters U, Hsu L, Gruber SB, Casey G, Schmit SL, O’Mara T, Spurdle AB, Thompson DJ, Tomlinson I, De Vivo I, Landi MT, Law MH, Iles MM, Demenais F, Kumar R, MacGregor S, Bishop DT, Ward SV, Bondy ML, Houlston R, Wiencke JK, Melin B, Barnholtz-Sloan J, Kinnersley B, Wrensch MR, Amos CI, Hung RJ, Brennan P, McKay J, Caporaso NE, Berndt SI, Birmann BM, Camp NJ, Kraft P, Rothman N, Slager SL, Berchuck A, Pharoah PDP, Sellers TA, Gayther SA, Pearce CL, Goode EL, Schildkraut JM, Moysich KB, Amundadottir LT, Jacobs EJ, Klein AP, Petersen GM, Risch HA, Stolzenberg-Solomon RZ, Wolpin BM, Li D, Eeles RA, Haiman CA, Kote-Jarai Z, Schumacher FR, Al Olama AA, Purdue MP, Scelo G, Dalgaard MD, Greene MH, Grotmol T, Kanetsky PA, McGlynn KA, Nathanson KL, Turnbull C, Wiklund F, Chanock S, Chatterjee N, Garcia-Closas M. Assessment of polygenic architecture and risk prediction based on common variants across fourteen cancers. Nature Communications 2020, 11: 3353. PMID: 32620889, PMCID: PMC7335068, DOI: 10.1038/s41467-020-16483-3.Peer-Reviewed Original Research
2017
Determining Risk of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on Epidemiologic Factors and Genetic Variants
Dong J, Buas MF, Gharahkhani P, Kendall BJ, Onstad L, Zhao S, Anderson LA, Wu AH, Ye W, Bird NC, Bernstein L, Chow WH, Gammon MD, Liu G, Caldas C, Pharoah PD, Risch HA, Iyer PG, Reid BJ, Hardie LJ, Lagergren J, Shaheen NJ, Corley DA, Fitzgerald RC, consortium S, Whiteman DC, Vaughan TL, Thrift AP. Determining Risk of Barrett’s Esophagus and Esophageal Adenocarcinoma Based on Epidemiologic Factors and Genetic Variants. Gastroenterology 2017, 154: 1273-1281.e3. PMID: 29247777, PMCID: PMC5880715, DOI: 10.1053/j.gastro.2017.12.003.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaArea Under CurveAustraliaBarrett EsophagusCase-Control StudiesDatabases, FactualDecision Support TechniquesEsophageal NeoplasmsEuropeFemaleGene-Environment InteractionGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansLife StyleLogistic ModelsMaleMiddle AgedModels, GeneticMolecular EpidemiologyMultifactorial InheritanceNorth AmericaOdds RatioPhenotypePolymorphism, Single NucleotidePredictive Value of TestsRisk AssessmentRisk FactorsROC CurveConceptsGastroesophageal reflux diseaseBarrett's esophagusEsophageal adenocarcinomaLifestyle factorsPolygenic risk scoresGERD symptomsNon-genetic factorsDemographic/lifestyle factorsNet reclassification improvementCharacteristic curve analysisAUC valuesRisk prediction modelEsophageal cancer studyInternational Barrett'sReflux diseaseHighest quartileNet reclassificationEpidemiologic factorsReclassification improvementLowest quartileHigh riskRisk scorePatientsEsophagusAbstractText
2016
Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data
Shi J, Park JH, Duan J, Berndt ST, Moy W, Yu K, Song L, Wheeler W, Hua X, Silverman D, Garcia-Closas M, Hsiung CA, Figueroa JD, Cortessis VK, Malats N, Karagas MR, Vineis P, Chang IS, Lin D, Zhou B, Seow A, Matsuo K, Hong YC, Caporaso NE, Wolpin B, Jacobs E, Petersen GM, Klein AP, Li D, Risch H, Sanders AR, Hsu L, Schoen RE, Brenner H, , , , , , , Stolzenberg-Solomon R, Gejman P, Lan Q, Rothman N, Amundadottir LT, Landi MT, Levinson DF, Chanock SJ, Chatterjee N. Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data. PLOS Genetics 2016, 12: e1006493. PMID: 28036406, PMCID: PMC5201242, DOI: 10.1371/journal.pgen.1006493.Peer-Reviewed Original ResearchConstrained Score Statistics Identify Genetic Variants Interacting with Multiple Risk Factors in Barrett’s Esophagus
Dai JY, de Dieu Tapsoba J, Buas MF, Consortium T, Chow W, Shaheen N, Anderson L, Corley D, Gammon M, Hardie L, Lagergren J, Whiteman D, Risch H, Vaughan T. Constrained Score Statistics Identify Genetic Variants Interacting with Multiple Risk Factors in Barrett’s Esophagus. American Journal Of Human Genetics 2016, 99: 352-365. PMID: 27486777, PMCID: PMC4974090, DOI: 10.1016/j.ajhg.2016.06.018.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAge FactorsBarrett EsophagusEsophageal NeoplasmsFemaleGastroesophageal RefluxGene-Environment InteractionGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyHumansMaleModels, GeneticObesityOdds RatioPolymorphism, Single NucleotideReproducibility of ResultsRisk FactorsSample SizeSex FactorsSmokingConceptsBarrett's esophagusEsophageal adenocarcinomaGene-environment interactionsMultiple risk factorsEsophageal Adenocarcinoma ConsortiumEnvironmental exposure dataGenetic variantsGastresophageal refluxTobacco smokingRisk factorsCancer epidemiologyEsophagusExposure dataAdenocarcinomaMultivariate gene-environment interactionsLow statistical powerTesting strategiesGenome-wide significanceSmokingObesityStatistical powerEpidemiologyReflux
2012
Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus
Su Z, Gay LJ, Strange A, Palles C, Band G, Whiteman DC, Lescai F, Langford C, Nanji M, Edkins S, van der Winkel A, Levine D, Sasieni P, Bellenguez C, Howarth K, Freeman C, Trudgill N, Tucker AT, Pirinen M, Peppelenbosch MP, van der Laan LJ, Kuipers EJ, Drenth JP, Peters WH, Reynolds JV, Kelleher DP, McManus R, Grabsch H, Prenen H, Bisschops R, Krishnadath K, Siersema PD, van Baal JW, Middleton M, Petty R, Gillies R, Burch N, Bhandari P, Paterson S, Edwards C, Penman I, Vaidya K, Ang Y, Murray I, Patel P, Ye W, Mullins P, Wu AH, Bird NC, Dallal H, Shaheen NJ, Murray LJ, Koss K, Bernstein L, Romero Y, Hardie LJ, Zhang R, Winter H, Corley DA, Panter S, Risch HA, Reid BJ, Sargeant I, Gammon MD, Smart H, Dhar A, McMurtry H, Ali H, Liu G, Casson AG, Chow WH, Rutter M, Tawil A, Morris D, Nwokolo C, Isaacs P, Rodgers C, Ragunath K, MacDonald C, Haigh C, Monk D, Davies G, Wajed S, Johnston D, Gibbons M, Cullen S, Church N, Langley R, Griffin M, Alderson D, Deloukas P, Hunt SE, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Anderson M, Brooks C, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood N, Trynka G, Wijmenga C, Cazier JB, Atherfold P, Nicholson AM, Gellatly NL, Glancy D, Cooper SC, Cunningham D, Lind T, Hapeshi J, Ferry D, Rathbone B, Brown J, Love S, Attwood S, MacGregor S, Watson P, Sanders S, Ek W, Harrison RF, Moayyedi P, de Caestecker J, Barr H, Stupka E, Vaughan TL, Peltonen L, Spencer CC, Tomlinson I, Donnelly P, Jankowski JA. Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus. Nature Genetics 2012, 44: 1131-1136. PMID: 22961001, PMCID: PMC3459818, DOI: 10.1038/ng.2408.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedBarrett EsophagusCase-Control StudiesChromosomes, Human, Pair 16FemaleGene FrequencyGenetic LociGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansLinkage DisequilibriumMajor Histocompatibility ComplexMaleMiddle AgedModels, GeneticPolymorphism, Single Nucleotide