Phenotype Harmonization in the GLIDE2 Oral Health Genomics Consortium.
Phenotype Harmonization in the GLIDE2 Oral Health Genomics Consortium.
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DOI：
10.1177/00220345221109775
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发表时间：
2022-10
影响因子：
7.6
通讯作者：
中科院分区：
文献类型：
--
作者：
遗传危险因素在口腔、牙齿和颅面疾病的病因学中起着重要作用。确定相关的风险位点并了解其分子生物学可以突出新的预防和管理途径。我们目前对口腔健康基因组学的理解表明，龋齿和牙周炎是多基因疾病，需要非常大的样本量和信息表型措施来发现信号并充分映射整个人类基因组的关联。在本文中，我们介绍了基因-生活方式相互作用和牙科终点联盟（GLIDE 2）的第二波，并讨论了相关的数据分析挑战，机遇和应用。在这一阶段，该联盟包括来自21项研究的70多万名参与者的多样化，多种族样本，这些研究提供了有关龋齿经验和牙周炎的临床数据。我们概述了从异质性人群的数据相结合的方法学挑战，以及在解决详细的临床检查记录到易处理的表型的数据减少的问题，并描述了一种策略，解决这个问题。具体而言，我们提出了一种3层表型分析方法，旨在利用联盟中的大样本量和一些研究中可用的详细临床信息，其中采用了二进制，严重程度涵盖和“精确”数据驱动的临床特征。作为在多个队列中使用数据驱动特征的说明，我们在8项参与研究（N = 55，143）中使用先前开发的恒牙列牙齿表面水平龋齿模式特征应用龋齿经验数据协调。我们证明，这些临床模式在多个队列中是可转移的，在每个研究中具有相似的相对贡献，因此是GLIDE 2扩展和多样化多种族样本中遗传询问的主要目标。我们预计GLIDE 2的结果将决定性地推进口腔，牙科和颅面健康和疾病机制的知识基础，并进一步促进基因组学研究中的国际合作以及数据和资源共享。
Genetic risk factors play important roles in the etiology of oral, dental, and craniofacial diseases. Identifying the relevant risk loci and understanding their molecular biology could highlight new prevention and management avenues. Our current understanding of oral health genomics suggests that dental caries and periodontitis are polygenic diseases, and very large sample sizes and informative phenotypic measures are required to discover signals and adequately map associations across the human genome. In this article, we introduce the second wave of the Gene-Lifestyle Interactions and Dental Endpoints consortium (GLIDE2) and discuss relevant data analytics challenges, opportunities, and applications. In this phase, the consortium comprises a diverse, multiethnic sample of over 700,000 participants from 21 studies contributing clinical data on dental caries experience and periodontitis. We outline the methodological challenges of combining data from heterogeneous populations, as well as the data reduction problem in resolving detailed clinical examination records into tractable phenotypes, and describe a strategy that addresses this. Specifically, we propose a 3-tiered phenotyping approach aimed at leveraging both the large sample size in the consortium and the detailed clinical information available in some studies, wherein binary, severity-encompassing, and “precision,” data-driven clinical traits are employed. As an illustration of the use of data-driven traits across multiple cohorts, we present an application of dental caries experience data harmonization in 8 participating studies (N = 55,143) using previously developed permanent dentition tooth surface–level dental caries pattern traits. We demonstrate that these clinical patterns are transferable across multiple cohorts, have similar relative contributions within each study, and thus are prime targets for genetic interrogation in the expanded and diverse multiethnic sample of GLIDE2. We anticipate that results from GLIDE2 will decisively advance the knowledge base of mechanisms at play in oral, dental, and craniofacial health and disease and further catalyze international collaboration and data and resource sharing in genomics research.
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影响因子：
64.8
作者：
Shungin, Dmitry;Winkler, Thomas W.;Croteau-Chonka, Damien C.;Ferreira, Teresa;Lockes, Adam E.;Maegi, Reedik;Strawbridge, Rona J.;Pers, Tune H.;Fischer, Krista;Justice, Anne E.;Workalemahu, Tsegaselassie;Wu, Joseph M. W.;Buchkovich, Martin L.;Heard-Costa, Nancy L.;Roman, Tamara S.;Drong, Alexander W.;Song, Ci;Gustafsson, Stefan;Day, Felix R.;Esko, Tonu;Fall, Tove;Kutalik, Zoltan;Luan, Jian'an;Randall, Joshua C.;Scherag, Andre;Vedantam, Sailaja;Wood, Andrew R.;Chen, Jin;Fehrmann, Rudolf;Karjalainen, Juha;Kahali, Bratati;Liu, Ching-Ti;Schmidt, Ellen M.;Absher, Devin;Amin, Najaf;Anderson, Denise;Beekman, Marian;Bragg-Gresham, Jennifer L.;Buyske, Steven;Demirkan, Ayse;Ehret, Georg B.;Feitosa, Mary F.;Goel, Anuj;Jackson, Anne U.;Johnson, Toby;Kleber, Marcus E.;Kristiansson, Kati;Mangino, Massimo;Leach, Irene Mateo;Medina-Gomez, Carolina;Palmer, Cameron D.;Pasko, Dorota;Pechlivaniss, Sonali;Peters, Marjolein J.;Prokopenko, Inga;Stancakova, Alena;Sung, Yun Ju;Tanakam, Toshiko;Teumer, Alexander;Van Vliet-Ostaptchouk, Jana V.;Yengo, Loic;Zhang, Weihua;Albrecht, Eva;Arnlov, Johan;Arscott, Gillian M.;Bandinelli, Stefania;Barrett, Amy;Bellis, Claire;Bennett, Amanda J.;Berne, Christian;Blueher, Matthias;Buhringer, Stefan;Bonnet, Fabrice;Boettcher, Yvonne;Bruinenberg, Marcel;Carba, Delia B.;Caspersen, Ida H.;Clarke, Robert;Daw, E. Warwick;Deelen, Joris;Deelman, Ewa;Delgado, Graciela;Doney, Alex S. F.;Eklund, Niina;Erdos, Michael R.;Estrada, Karol;Eury, Elodie;Friedrichs, Nele;Garcia, Melissa E.;Giedraitis, Vilmantas;Gigante, Bruna;Go, Alan S.;Golay, Alain;Grallert, Harald;Grammer, Tanja B.;Graessler, Juergen;Grewal, Jagvir;Groves, Christopher J.;Haller, Toomas;Hallmans, Goran;Hartman, Catharina A.;Hassinen, Maija;Hayward, Caroline;Heikkila, Kauko;Herzig, Karl-Heinz;Helmer, Quinta;Hillege, Hans L.;Holmen, Oddgeir;Hunt, Steven C.;Isaacs, Aaron;Ittermann, Till;James, Alan L.;Johansson, Ingegerd;Juliusdottir, Thorhildur;Kalafati, Ioanna-Panagiota;Kinnunen, Leena;Koenig, Wolfgang;Kooner, Ishminder K.;Kratzer, Wolfgang;Lamina, Claudia;Leander, Karin;Lee, Nanette R.;Lichtner, Peter;Lind, Lars;Lindstrom, Jaana;Lobbens, Stephane;Lorentzon, Mattias;Mach, Francois;Magnusson, Patrik K. E.;Mahajan, Anubha;McArdle, Wendy L.;Menni, Cristina;Merger, Sigrun;Mihailov, Evelin;Milani, Lili;Mills, Rebecca;Moayyeri, Alireza;Monda, Ken L.;Mooijaart, Simon P.;Muehleisen, Thomas W.;Mulas, Antonella;Mueller, Gabriele;Mueller-Nurasyid, Martina;Nagaraja, Ramaiah;Nalls, Michael A.;Narisu, Narisu;Glorioso, Nicola;Nolte, Ilja M.;Olden, Matthias;Rayner, Nigel W.;Renstrom, Frida;Ried, Janina S.;Robertson, Neil R.;Rose, Lynda M.;Sanna, Serena;Scharnagl, Hubert;Scholtens, Salome;Sennblad, Bengt;Seufferlein, Thomas;Sitlani, Colleen M.;Smith, Albert Vernon;Stirrups, Kathleen;Stringham, Heather M.;Sundstrom, Johan;Swertz, Morris A.;Swift, Amy J.;Syvanen, Ann-Christine;Tayo, Bamidele O.;Thorand, Barbara;Thorleifsson, Gudmar;Tomaschitz, Andreas;Troffa, Chiara;van Oort, Floor V. A.;Verweij, Niek;Vonk, Judith M.;Waite, Lindsay L.;Wennauer, Roman;Wilsgaard, Tom;Wojczynski, Mary K.;Wong, Andrew;Zhang, Qunyuan;Zhao, Jing Hua;Brennan, Eoin P.;Choi, Murim;Eriksson, Per;Folkersen, Lasse;Franco-Cereceda, Anders;Gharavi, Ali G.;Hedman, Asa K.;Hivert, Marie-France;Huang, Jinyan;Kanoni, Stavroula;Karpe, Fredrik;Keildson, Sarah;Kiryluk, Krzysztof;Liang, Liming;Lifton, Richard P.;Ma, Baoshan;McKnight, Amy J.;McPherson, Ruth;Metspalu, Andres;Min, Josine L.;Moffatt, Miriam F.;Montgomery, Grant W.;Murabito, Joanne M.;Nicholson, George;Nyholt, Dale R.;Olsson, Christian;Perry, John R. B.;Reinmaa, Eva;Salem, Rany M.;Sandholm, Niina;Schadt, Eric E.;Scott, Robert A.;Stolk, Lisette;Vallejo, Edgar E.;Westra, Harm-Jan;Zondervan, Krina T.;Amouyel, Philippe;Arveiler, Dominique;Bakker, Stephan J. L.;Beilby, John;Bergman, Richard N.;Blangero, John;Brown, Morris J.;Burnier, Michel;Campbell, Harry;Chakravarti, Aravinda;Chiness, Peter S.;Claudi-Boehmi, Simone;Collins, Francis S.;Crawford, Dana C.;Danesh, John;de Faire, Ulf;de Geusl, Eco J. C.;Doerr, Marcus;Erbel, Raimund;Eriksson, Johan G.;Farrall, Martin;Ferrannini, Ele;Ferrieres, Jean;Forouhi, Nita G.;Forrester, Terrence;Franco, Oscar H.;Gansevoort, Ron T.;Gieger, Christian;Gudnason, Vilmundur;Haiman, Christopher A.;Harris, Tamara B.;Hattersley, Andrew T.;Heliovaara, Markku;Hicks, Andrew A.;Hingorani, Aroon D.;Hoffmann, Wolfgang;Hofman, Albert;Homuth, Georg;Humphries, Steve E.;Hyppoenen, Elina;Illig, Thomas;Jarvelin, Marjo-Riitta;Johansen, Berit;Jousilahti, Pekka;Jula, Antti M.;Kaprio, Jaakko;Kee, Frank;Keinanen-Kiukaanniemi, Sirkka M.;Kooner, Jaspal S.;Kooperberg, Charles;Kovacs, Peter;Kraja, Aldi T.;Kumari, Meena;Kuulasmaa, Kari;Kuusisto, Johanna;Lakka, Timo A.;Langenberg, Claudia;Le Marchand, Loic;Lehtimaki, Terho;Lyssenko, Valeriya;Mannisto, Satu;Marette, Andre;Matise, Tara C.;McKenzie, Colin A.;McKnight, Barbara;Musk, Arthur W.;Mohlenkamp, Stefan;Morris, Andrew D.;Nelis, Mari;Ohlsson, Claes;Oldehinkel, Albertine J.;Ong, Ken K.;Palmer, Lyle J.;Penninx, Brenda W.;Peters, Annette;Pramstaller, Peter P.;Raitakari, Olli T.;Rankinen, Tuomo;Rao, D. C.;Rice, Treva K.;Ridker, Paul M.;Ritchie, Marylyn D.;Rudan, Igor;Salomaa, Veikko;Samani, Nilesh J.;Saramies, Jouko;Sarzynski, Mark A.;Schwarz, Peter E. H.;Shuldiner, Alan R.;Staessen, Jan A.;Steinthorsdottir, Valgerdur;Stolk, Ronald P.;Strauch, Konstantin;Toenjes, Anke;Tremblay, Angelo;Tremoli, Elena;Vohl, Marie-Claude;Voelker, Uwe;Vollenweider, Peter;Wilson, James F.;Witteman, Jacqueline C.;Adair, Linda S.;Bochud, Murielle;Boehm, Bernhard O.;Bornstein, Stefan R.;Bouchard, Claude;Cauchi, Stephane;Caulfield, Mark J.;Chambers, John C.;Chasman, Daniel I.;Cooper, Richard S.;Dedoussis, George;Ferrucci, Luigi;Froguel, Philippe;Grabe, Hans-Joergen;Hamsten, Anders;Hui, Jennie;Hveem, Kristian;Joeckel, Karl-Heinz;Kivimaki, Mika;Kuh, Diana;Laakso, Markku;Liu, Yongmei;Maerz, Winfried;Munroe, Patricia B.;Njolstad, Inger;Oostra, Ben A.;Palmer, Colin N. A.;Pedersen, Nancy L.;Perola, Markus;Perusse, Louis;Peters, Ulrike;Power, Chris;Quertermous, Thomas;Rauramaa, Rainer;Rivadeneira, Fernando;Saaristo, Timo E.;Saleheen, Danish;Sinisalo, Juha;Slagboom, P. Eline;Snieder, Harold;Spector, Tim D.;Thorsteinsdottir, Unnur R.;Stumvoll, Michael;Tuomilehto, Jaakko;Uitterlinden, Andre G.;Uusitupa, Math;van der Harst, Pim;Veronesi, Giovanni;Walker, Mark;Wareham, Nicholas J.;Watkins, Hugh;Wichmann, H-Erich;Abecasis, Goncalo R.;Assimes, Themistocles L.;Berndt, Sonja I.;Boehnkes, Michael;Borecki, Ingrid B.;Deloukas, Panos;Franke, Lude;Frayling, Timothy M.;Groop, Leif C.;Hunter, David J.;Kaplan, Robert C.;O'Connell, Jeffrey R.;Qi, Lu;Schlessinger, David;Strachan, David P.;Stefansson, Kari;van Dujin, Cornelia M.;Willer, Cristen J.;Visscher, Peter M.;Yang, Jian;Hirschhorn, Joel N.;Zillikens, M. Carola;McCarthy, Mark I.;Speliotes, Elizabeth K.;North, Kari E.;Fox, Caroline S.;Barroso, Ines;Franks, Paul W.;Ingelsson, Erik;Heid, Iris M.;Loos, Ruth J. F.;Cupples, L. Adrienne;Morris, Andrew P.;Lindgren, Cecilia M.;Mohlke, Karen L.
通讯作者：
Mohlke, Karen L.
影响因子：
2.9
作者：
Shaffer, John R.;Feingold, Eleanor;Marazita, Mary L.
通讯作者：
Marazita, Mary L.
影响因子：
2.3
作者：
Haworth S;Shungin D;Kwak SY;Kim HY;West NX;Thomas SJ;Franks PW;Timpson NJ;Shin MJ;Johansson I
通讯作者：
Johansson I
影响因子：
64.8
作者：
Graham SE;Clarke SL;Wu KH;Kanoni S;Zajac GJM;Ramdas S;Surakka I;Ntalla I;Vedantam S;Winkler TW;Locke AE;Marouli E;Hwang MY;Han S;Narita A;Choudhury A;Bentley AR;Ekoru K;Verma A;Trivedi B;Martin HC;Hunt KA;Hui Q;Klarin D;Zhu X;Thorleifsson G;Helgadottir A;Gudbjartsson DF;Holm H;Olafsson I;Akiyama M;Sakaue S;Terao C;Kanai M;Zhou W;Brumpton BM;Rasheed H;Ruotsalainen SE;Havulinna AS;Veturi Y;Feng Q;Rosenthal EA;Lingren T;Pacheco JA;Pendergrass SA;Haessler J;Giulianini F;Bradford Y;Miller JE;Campbell A;Lin K;Millwood IY;Hindy G;Rasheed A;Faul JD;Zhao W;Weir DR;Turman C;Huang H;Graff M;Mahajan A;Brown MR;Zhang W;Yu K;Schmidt EM;Pandit A;Gustafsson S;Yin X;Luan J;Zhao JH;Matsuda F;Jang HM;Yoon K;Medina-Gomez C;Pitsillides A;Hottenga JJ;Willemsen G;Wood AR;Ji Y;Gao Z;Haworth S;Mitchell RE;Chai JF;Aadahl M;Yao J;Manichaikul A;Warren HR;Ramirez J;Bork-Jensen J;Kårhus LL;Goel A;Sabater-Lleal M;Noordam R;Sidore C;Fiorillo E;McDaid AF;Marques-Vidal P;Wielscher M;Trompet S;Sattar N;Møllehave LT;Thuesen BH;Munz M;Zeng L;Huang J;Yang B;Poveda A;Kurbasic A;Lamina C;Forer L;Scholz M;Galesloot TE;Bradfield JP;Daw EW;Zmuda JM;Mitchell JS;Fuchsberger C;Christensen H;Brody JA;Feitosa MF;Wojczynski MK;Preuss M;Mangino M;Christofidou P;Verweij N;Benjamins JW;Engmann J;Kember RL;Slieker RC;Lo KS;Zilhao NR;Le P;Kleber ME;Delgado GE;Huo S;Ikeda DD;Iha H;Yang J;Liu J;Leonard HL;Marten J;Schmidt B;Arendt M;Smyth LJ;Cañadas-Garre M;Wang C;Nakatochi M;Wong A;Hutri-Kähönen N;Sim X;Xia R;Huerta-Chagoya A;Fernandez-Lopez JC;Lyssenko V;Ahmed M;Jackson AU;Yousri NA;Irvin MR;Oldmeadow C;Kim HN;Ryu S;Timmers PRHJ;Arbeeva L;Dorajoo R;Lange LA;Chai X;Prasad G;Lorés-Motta L;Pauper M;Long J;Li X;Theusch E;Takeuchi F;Spracklen CN;Loukola A;Bollepalli S;Warner SC;Wang YX;Wei WB;Nutile T;Ruggiero D;Sung YJ;Hung YJ;Chen S;Liu F;Yang J;Kentistou KA;Gorski M;Brumat M;Meidtner K;Bielak LF;Smith JA;Hebbar P;Farmaki AE;Hofer E;Lin M;Xue C;Zhang J;Concas MP;Vaccargiu S;van der Most PJ;Pitkänen N;Cade BE;Lee J;van der Laan SW;Chitrala KN;Weiss S;Zimmermann ME;Lee JY;Choi HS;Nethander M;Freitag-Wolf S;Southam L;Rayner NW;Wang CA;Lin SY;Wang JS;Couture C;Lyytikäinen LP;Nikus K;Cuellar-Partida G;Vestergaard H;Hildalgo B;Giannakopoulou O;Cai Q;Obura MO;van Setten J;Li X;Schwander K;Terzikhan N;Shin JH;Jackson RD;Reiner AP;Martin LW;Chen Z;Li L;Highland HM;Young KL;Kawaguchi T;Thiery J;Bis JC;Nadkarni GN;Launer LJ;Li H;Nalls MA;Raitakari OT;Ichihara S;Wild SH;Nelson CP;Campbell H;Jäger S;Nabika T;Al-Mulla F;Niinikoski H;Braund PS;Kolcic I;Kovacs P;Giardoglou T;Katsuya T;Bhatti KF;de Kleijn D;de Borst GJ;Kim EK;Adams HHH;Ikram MA;Zhu X;Asselbergs FW;Kraaijeveld AO;Beulens JWJ;Shu XO;Rallidis LS;Pedersen O;Hansen T;Mitchell P;Hewitt AW;Kähönen M;Pérusse L;Bouchard C;Tönjes A;Chen YI;Pennell CE;Mori TA;Lieb W;Franke A;Ohlsson C;Mellström D;Cho YS;Lee H;Yuan JM;Koh WP;Rhee SY;Woo JT;Heid IM;Stark KJ;Völzke H;Homuth G;Evans MK;Zonderman AB;Polasek O;Pasterkamp G;Hoefer IE;Redline S;Pahkala K;Oldehinkel AJ;Snieder H;Biino G;Schmidt R;Schmidt H;Chen YE;Bandinelli S;Dedoussis G;Thanaraj TA;Kardia SLR;Kato N;Schulze MB;Girotto G;Jung B;Böger CA;Joshi PK;Bennett DA;De Jager PL;Lu X;Mamakou V;Brown M;Caulfield MJ;Munroe PB;Guo X;Ciullo M;Jonas JB;Samani NJ;Kaprio J;Pajukanta P;Adair LS;Bechayda SA;de Silva HJ;Wickremasinghe AR;Krauss RM;Wu JY;Zheng W;den Hollander AI;Bharadwaj D;Correa A;Wilson JG;Lind L;Heng CK;Nelson AE;Golightly YM;Wilson JF;Penninx B;Kim HL;Attia J;Scott RJ;Rao DC;Arnett DK;Hunt SC;Walker M;Koistinen HA;Chandak GR;Yajnik CS;Mercader JM;Tusié-Luna T;Aguilar-Salinas CA;Villalpando CG;Orozco L;Fornage M;Tai ES;van Dam RM;Lehtimäki T;Chaturvedi N;Yokota M;Liu J;Reilly DF;McKnight AJ;Kee F;Jöckel KH;McCarthy MI;Palmer CNA;Vitart V;Hayward C;Simonsick E;van Duijn CM;Lu F;Qu J;Hishigaki H;Lin X;März W;Parra EJ;Cruz M;Gudnason V;Tardif JC;Lettre G;'t Hart LM;Elders PJM;Damrauer SM;Kumari M;Kivimaki M;van der Harst P;Spector TD;Loos RJF;Province MA;Psaty BM;Brandslund I;Pramstaller PP;Christensen K;Ripatti S;Widén E;Hakonarson H;Grant SFA;Kiemeney LALM;de Graaf J;Loeffler M;Kronenberg F;Gu D;Erdmann J;Schunkert H;Franks PW;Linneberg A;Jukema JW;Khera AV;Männikkö M;Jarvelin MR;Kutalik Z;Cucca F;Mook-Kanamori DO;van Dijk KW;Watkins H;Strachan DP;Grarup N;Sever P;Poulter N;Rotter JI;Dantoft TM;Karpe F;Neville MJ;Timpson NJ;Cheng CY;Wong TY;Khor CC;Sabanayagam C;Peters A;Gieger C;Hattersley AT;Pedersen NL;Magnusson PKE;Boomsma DI;de Geus EJC;Cupples LA;van Meurs JBJ;Ghanbari M;Gordon-Larsen P;Huang W;Kim YJ;Tabara Y;Wareham NJ;Langenberg C;Zeggini E;Kuusisto J;Laakso M;Ingelsson E;Abecasis G;Chambers JC;Kooner JS;de Vries PS;Morrison AC;North KE;Daviglus M;Kraft P;Martin NG;Whitfield JB;Abbas S;Saleheen D;Walters RG;Holmes MV;Black C;Smith BH;Justice AE;Baras A;Buring JE;Ridker PM;Chasman DI;Kooperberg C;Wei WQ;Jarvik GP;Namjou B;Hayes MG;Ritchie MD;Jousilahti P;Salomaa V;Hveem K;Åsvold BO;Kubo M;Kamatani Y;Okada Y;Murakami Y;Thorsteinsdottir U;Stefansson K;Ho YL;Lynch JA;Rader DJ;Tsao PS;Chang KM;Cho K;O'Donnell CJ;Gaziano JM;Wilson P;Rotimi CN;Hazelhurst S;Ramsay M;Trembath RC;van Heel DA;Tamiya G;Yamamoto M;Kim BJ;Mohlke KL;Frayling TM;Hirschhorn JN;Kathiresan S;VA Million Veteran Program;Global Lipids Genetics Consortium*;Boehnke M;Natarajan P;Peloso GM;Brown CD;Morris AP;Assimes TL;Deloukas P;Sun YV;Willer CJ
通讯作者：
Willer CJ
DOI：
10.1007/978-1-4939-9012-2_38
发表时间：
2019-01-01
期刊：
ODONTOGENESIS
影响因子：
--
作者：
Agler, Cary S.;Shungin, Dmitry;Divaris, Kimon
通讯作者：
Divaris, Kimon