2024
Balancing the efforts of chart review and gains in PRS prediction accuracy: An empirical study
Lei Y, Christian Naj A, Xu H, Li R, Chen Y. Balancing the efforts of chart review and gains in PRS prediction accuracy: An empirical study. Journal Of Biomedical Informatics 2024, 157: 104705. PMID: 39134233, DOI: 10.1016/j.jbi.2024.104705.Peer-Reviewed Original ResearchAlzheimer's Disease Genetics ConsortiumChart reviewPRS modelCase-control datasetGenetic association analysisGenetics ConsortiumPhenotype misclassificationSimulated phenotypesPhenotypic dataAssociation analysisEstimation of associated parametersBias reduction methodMedian thresholdPhenotypeMisclassification rateOriginal phenotypeDiverse arrayChartsMisclassificationGenotypesReviewEffects of biasBiasPrediction modelPRS
2021
Novel Alzheimer Disease Risk Loci and Pathways in African American Individuals Using the African Genome Resources Panel
Kunkle BW, Schmidt M, Klein HU, Naj AC, Hamilton-Nelson KL, Larson EB, Evans DA, De Jager PL, Crane PK, Buxbaum JD, Ertekin-Taner N, Barnes LL, Fallin MD, Manly JJ, Go RCP, Obisesan TO, Kamboh MI, Bennett DA, Hall KS, Goate AM, Foroud TM, Martin ER, Wang L, Byrd GS, Farrer LA, Haines JL, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C, Abner E, Adams P, Albin R, Apostolova L, Arnold S, Atwood C, Baldwin C, Barber R, Barral S, Beach T, Becker J, Beecham G, Bigio E, Bird T, Blacker D, Boeve B, Bowen J, Boxer A, Burke J, Burns J, Cairns N, Cao C, Carlsson C, Carney R, Carrasquillo M, Cribbs D, Cruchaga C, Dick M, Dickson D, Doody R, Duara R, Faber K, Fairchild T, Fallon K, Fardo D, Farlow M, Ferris S, Frosch M, Galasko D, Gearing M, Geschwind D, Ghetti B, Gilbert J, Green R, Growdon J, Hakonarson H, Hamilton R, Hardy J, Harrell L, Honig L, Huebinger R, Huentelman M, Hulette C, Jarvik G, Jin L, Karydas A, Katz M, Kauwe J, Keene C, Kim R, Kramer J, Lah J, Leung Y, Li G, Lieberman A, Lipton R, Lyketsos C, Malamon J, Marson D, Martiniuk F, Masliah E, McCormick W, McCurry S, McDavid A, McDonough S, McKee A, Mesulam M, Miller B, Miller C, Montine T, Mukherjee S, Myers A, O’Bryant S, Olichney J, Parisi J, Peskind E, Pierce A, Poon W, Potter H, Qu L, Quinn J, Raj A, Raskind M, Reisberg B, Reisch J, Ringman J, Roberson E, Rogaeva E, Rosen H, Royall D, Sager M, Schneider J, Schneider L, Seeley W, Small S, Sonnen J, Spina S, St George-Hyslop P, Stern R, Tanzi R, Troncoso J, Tsuang D, Valladares O, Van Deerlin V, Vardarajan B, Vinters H, Vonsattel J, Weintraub S, Welsh-Bohmer K, Wilhelmsen K, Williamson J, Wingo T, Woltjer R, Wu C, Younkin S, Yu L, Yu C, Zhao Y, Graff-Radford N, Martinez I, Ayodele T, Logue M, Cantwell L, Jean-Francois M, Kuzma A, Adams L, Vance J, Cuccaro M, Chung J, Mez J, Lunetta K, Jun G, Lopez O, Hendrie H, Reiman E, Kowall N, Leverenz J, Small S, Levey A, Golde T, Saykin A, Starks T, Albert M, Hyman B, Petersen R, Sano M, Wisniewski T, Vassar R, Kaye J, Henderson V, DeCarli C, LaFerla F, Brewer J, Miller B, Swerdlow R, Van Eldik L, Paulson H, Trojanowski J, Chui H, Rosenberg R, Craft S, Grabowski T, Asthana S, Morris J, Strittmatter S, Kukull W. Novel Alzheimer Disease Risk Loci and Pathways in African American Individuals Using the African Genome Resources Panel. JAMA Neurology 2021, 78: 102-113. PMID: 33074286, PMCID: PMC7573798, DOI: 10.1001/jamaneurol.2020.3536.Peer-Reviewed Original ResearchConceptsIntergenic lociRisk lociAlzheimer's disease genome-wide association studiesGenome-wide association studiesGenome-wide associationDisease-associated lociAlzheimer's Disease Genetics ConsortiumDisease risk lociLargest association analysisAdditional risk lociAlzheimer’s disease risk lociGene expression dataTrafficking pathwaysAdditional lociPathway analysisAssociation studiesExpression dataAssociation analysisSuggestive significanceLociFamily-based data setCommon locusNovel mechanismAlzheimer's disease etiologyGenetics Consortium
2016
Genetic variants in CETP increase risk of intracerebral hemorrhage
Anderson CD, Falcone GJ, Phuah C, Radmanesh F, Brouwers HB, Battey TW, Biffi A, Peloso GM, Liu DJ, Ayres AM, Goldstein JN, Viswanathan A, Greenberg SM, Selim M, Meschia JF, Brown DL, Worrall BB, Silliman SL, Tirschwell DL, Flaherty ML, Kraft P, Jagiella JM, Schmidt H, Hansen BM, Jimenez‐Conde J, Giralt‐Steinhauer E, Elosua R, Cuadrado‐Godia E, Soriano C, van Nieuwenhuizen K, Klijn CJ, Rannikmae K, Samarasekera N, Salman R, Sudlow CL, Deary IJ, Morotti A, Pezzini A, Pera J, Urbanik A, Pichler A, Enzinger C, Norrving B, Montaner J, Fernandez‐Cadenas I, Delgado P, Roquer J, Lindgren A, Slowik A, Schmidt R, Kidwell CS, Kittner SJ, Waddy SP, Langefeld CD, Abecasis G, Willer CJ, Kathiresan S, Woo D, Rosand J, Consortium O. Genetic variants in CETP increase risk of intracerebral hemorrhage. Annals Of Neurology 2016, 80: 730-740. PMID: 27717122, PMCID: PMC5115931, DOI: 10.1002/ana.24780.Peer-Reviewed Original ResearchConceptsGenetic variantsCandidate gene analysisDNA sequence variantsGlobal Lipids Genetics ConsortiumDNA sequencesOngoing therapeutic developmentsSequence variantsIndependent variantsNominal associationCETP locusGenetics ConsortiumEuropean ancestryCETP variantsLociTherapeutic developmentVariantsGenetic risk scoreCETPDiscovery cohortGenetic scoreAncestryReplicationSequenceAnn NeurolAdverse cerebrovascular outcomes
2014
The Tourette International Collaborative Genetics (TIC Genetics) study, finding the genes causing Tourette syndrome: objectives and methods
Dietrich A, Fernandez TV, King RA, State MW, Tischfield JA, Hoekstra PJ, Heiman GA, the TIC Genetics Collaborative Group. The Tourette International Collaborative Genetics (TIC Genetics) study, finding the genes causing Tourette syndrome: objectives and methods. European Child & Adolescent Psychiatry 2014, 24: 141-151. PMID: 24771252, PMCID: PMC4209328, DOI: 10.1007/s00787-014-0543-x.Peer-Reviewed Original ResearchConceptsGenetic studiesSimilar genetic architectureGene discovery effortsMultiply affected pedigreesSingle major geneParent-child triosGenetic architectureMultigenic inheritanceDe novo mutationsMajor geneGenomic researchCollaborative Genetics StudyAffected pedigreesDiscovery effortsGenetic variantsGenetic contributionGenetics ConsortiumNovo mutationsGenesRare variantsBroader scientific communityGenetic riskRecent progressGeneticsVariantsA genome-wide association study of anorexia nervosa
Boraska V, Franklin C, Floyd J, Thornton L, Huckins L, Southam L, Rayner N, Tachmazidou I, Klump K, Treasure J, Lewis C, Schmidt U, Tozzi F, Kiezebrink K, Hebebrand J, Gorwood P, Adan R, Kas M, Favaro A, Santonastaso P, Fernández-Aranda F, Gratacos M, Rybakowski F, Dmitrzak-Weglarz M, Kaprio J, Keski-Rahkonen A, Raevuori A, Van Furth E, Slof-Op 't Landt M, Hudson J, Reichborn-Kjennerud T, Knudsen G, Monteleone P, Kaplan A, Karwautz A, Hakonarson H, Berrettini W, Guo Y, Li D, Schork N, Komaki G, Ando T, Inoko H, Esko T, Fischer K, Männik K, Metspalu A, Baker J, Cone R, Dackor J, DeSocio J, Hilliard C, O'Toole J, Pantel J, Szatkiewicz J, Taico C, Zerwas S, Trace S, Davis O, Helder S, Bühren K, Burghardt R, de Zwaan M, Egberts K, Ehrlich S, Herpertz-Dahlmann B, Herzog W, Imgart H, Scherag A, Scherag S, Zipfel S, Boni C, Ramoz N, Versini A, Brandys M, Danner U, de Kovel C, Hendriks J, Koeleman B, Ophoff R, Strengman E, van Elburg A, Bruson A, Clementi M, Degortes D, Forzan M, Tenconi E, Docampo E, Escaramís G, Jiménez-Murcia S, Lissowska J, Rajewski A, Szeszenia-Dabrowska N, Slopien A, Hauser J, Karhunen L, Meulenbelt I, Slagboom P, Tortorella A, Maj M, Dedoussis G, Dikeos D, Gonidakis F, Tziouvas K, Tsitsika A, Papezova H, Slachtova L, Martaskova D, Kennedy J, Levitan R, Yilmaz Z, Huemer J, Koubek D, Merl E, Wagner G, Lichtenstein P, Breen G, Cohen-Woods S, Farmer A, McGuffin P, Cichon S, Giegling I, Herms S, Rujescu D, Schreiber S, Wichmann H, Dina C, Sladek R, Gambaro G, Soranzo N, Julia A, Marsal S, Rabionet R, Gaborieau V, Dick D, Palotie A, Ripatti S, Widén E, Andreassen O, Espeseth T, Lundervold A, Reinvang I, Steen V, Le Hellard S, Mattingsdal M, Ntalla I, Bencko V, Foretova L, Janout V, Navratilova M, Gallinger S, Pinto D, Scherer S, Aschauer H, Carlberg L, Schosser A, Alfredsson L, Ding B, Klareskog L, Padyukov L, Courtet P, Guillaume S, Jaussent I, Finan C, Kalsi G, Roberts M, Logan D, Peltonen L, Ritchie G, Barrett J, Estivill X, Hinney A, Sullivan P, Collier D, Zeggini E, Bulik C. A genome-wide association study of anorexia nervosa. Molecular Psychiatry 2014, 19: 1085-1094. PMID: 24514567, PMCID: PMC4325090, DOI: 10.1038/mp.2013.187.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAssociation studiesGenome-wide significanceReplicate data setsCase-control sampleReplicated genotypesGlobal meta-analysisIntronic variantsGenetics ConsortiumGene studiesEuropean ancestryDe novoIn silicoAN casesAnorexia nervosaReplicationMeta-analyzedMeta-analysisSPATA13Discovery dataFAM124BReplicate resultsLower body weightCul3Discovery
2013
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis
Beecham A, Patsopoulos N, Xifara D, Davis M, Kemppinen A, Cotsapas C, Shah T, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo H, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg J, Hintzen R, Barcellos L, Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard H, Baker A, Band G, Baranzini S, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder T, Blackburn H, Bomfim I, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier S, Camu W, Carpentier W, Cavalla P, Celius E, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree B, Cusi D, Damotte V, Defer G, Delgado S, Deloukas P, di Sapio A, Dilthey A, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich I, Galimberti D, Gieger C, Gourraud P, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt S, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee M, Leone M, Leppä V, Liberatore G, Lie B, Lill C, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique C, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero I, Mescheriakova J, Moutsianas L, Myhr K, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price S, Quach H, Reunanen M, Robberecht W, Robertson N, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud N, Sellebjerg F, Selter R, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen P, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser E, Vucic S, Westerlind H, Wiley J, Wilkins A, Wilson J, Winkelmann J, Zajicek J, Zindler E, Haines J, Pericak-Vance M, Ivinson A, Stewart G, Hafler D, Hauser S, Compston A, McVean G, De Jager P, Sawcer S, McCauley J. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nature Genetics 2013, 45: 1353-1360. PMID: 24076602, PMCID: PMC3832895, DOI: 10.1038/ng.2770.Peer-Reviewed Original Research
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