Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR.
Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR.
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DOI：
10.1093/bioinformatics/btaa568
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发表时间：
2020-09-15
期刊：
影响因子：
--
通讯作者：
Dale AM
中科院分区：
文献类型：
--
作者：
Shadrin AA;Frei O;Smeland OB;Bettella F;O'Connell KS;Gani O;Bahrami S;Uggen TKE;Djurovic S;Holland D;Andreassen OA;Dale AM
确定功能遗传类别的相对贡献是理解复杂人类特征和疾病的遗传病因学的基础。在这里，我们提出了注释Informed-MiXeR，这是一种基于可能性的方法，用于使用全基因组关联研究的汇总统计量来估计影响表型的变体数量及其在基因组的不同功能注释类别中的效应大小。广泛的模拟表明，该模型是有效的广泛的遗传结构。该模型表明，复杂的人类表型在因果变异的数量、它们在基因组中的定位以及它们的效应大小方面存在很大差异。具体来说，蛋白质编码基因的外显子含有超过90%的影响2型糖尿病和炎症性肠病的变体，使其成为全外显子组研究的良好候选者。相比之下，精神分裂症、双相情感障碍和注意力缺陷/多动障碍的病因变异中<10%位于蛋白质编码外显子，表明调节机制在这些疾病的发病机制中发挥更重要的作用。该软件可在https://github.com/precimed/mixer上获得。 补充数据可在Bioinformatics在线获得。
Determining the relative contributions of functional genetic categories is fundamental to understanding the genetic etiology of complex human traits and diseases. Here, we present Annotation Informed-MiXeR, a likelihood-based method for estimating the number of variants influencing a phenotype and their effect sizes across different functional annotation categories of the genome using summary statistics from genome-wide association studies. Extensive simulations demonstrate that the model is valid for a broad range of genetic architectures. The model suggests that complex human phenotypes substantially differ in the number of causal variants, their localization in the genome and their effect sizes. Specifically, the exons of protein-coding genes harbor more than 90% of variants influencing type 2 diabetes and inflammatory bowel disease, making them good candidates for whole-exome studies. In contrast, <10% of the causal variants for schizophrenia, bipolar disorder and attention-deficit/hyperactivity disorder are located in protein-coding exons, indicating a more substantial role of regulatory mechanisms in the pathogenesis of these disorders. The software is available at: https://github.com/precimed/mixer. Supplementary data are available at Bioinformatics online.
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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.
基因发现和多基因预测，从基因组全基因组协会的教育程度研究中，有110万个人。
影响因子：
30.8
作者：
Lee JJ;Wedow R;Okbay A;Kong E;Maghzian O;Zacher M;Nguyen-Viet TA;Bowers P;Sidorenko J;Karlsson Linnér R;Fontana MA;Kundu T;Lee C;Li H;Li R;Royer R;Timshel PN;Walters RK;Willoughby EA;Yengo L;23andMe Research Team;COGENT (Cognitive Genomics Consortium);Social Science Genetic Association Consortium;Alver M;Bao Y;Clark DW;Day FR;Furlotte NA;Joshi PK;Kemper KE;Kleinman A;Langenberg C;Mägi R;Trampush JW;Verma SS;Wu Y;Lam M;Zhao JH;Zheng Z;Boardman JD;Campbell H;Freese J;Harris KM;Hayward C;Herd P;Kumari M;Lencz T;Luan J;Malhotra AK;Metspalu A;Milani L;Ong KK;Perry JRB;Porteous DJ;Ritchie MD;Smart MC;Smith BH;Tung JY;Wareham NJ;Wilson JF;Beauchamp JP;Conley DC;Esko T;Lehrer SF;Magnusson PKE;Oskarsson S;Pers TH;Robinson MR;Thom K;Watson C;Chabris CF;Meyer MN;Laibson DI;Yang J;Johannesson M;Koellinger PD;Turley P;Visscher PM;Benjamin DJ;Cesarini D
通讯作者：
Cesarini D
影响因子：
30.8
作者：
Mahajan A;Taliun D;Thurner M;Robertson NR;Torres JM;Rayner NW;Payne AJ;Steinthorsdottir V;Scott RA;Grarup N;Cook JP;Schmidt EM;Wuttke M;Sarnowski C;Mägi R;Nano J;Gieger C;Trompet S;Lecoeur C;Preuss MH;Prins BP;Guo X;Bielak LF;Below JE;Bowden DW;Chambers JC;Kim YJ;Ng MCY;Petty LE;Sim X;Zhang W;Bennett AJ;Bork-Jensen J;Brummett CM;Canouil M;Ec Kardt KU;Fischer K;Kardia SLR;Kronenberg F;Läll K;Liu CT;Locke AE;Luan J;Ntalla I;Nylander V;Schönherr S;Schurmann C;Yengo L;Bottinger EP;Brandslund I;Christensen C;Dedoussis G;Florez JC;Ford I;Franco OH;Frayling TM;Giedraitis V;Hackinger S;Hattersley AT;Herder C;Ikram MA;Ingelsson M;Jørgensen ME;Jørgensen T;Kriebel J;Kuusisto J;Ligthart S;Lindgren CM;Linneberg A;Lyssenko V;Mamakou V;Meitinger T;Mohlke KL;Morris AD;Nadkarni G;Pankow JS;Peters A;Sattar N;Stančáková A;Strauch K;Taylor KD;Thorand B;Thorleifsson G;Thorsteinsdottir U;Tuomilehto J;Witte DR;Dupuis J;Peyser PA;Zeggini E;Loos RJF;Froguel P;Ingelsson E;Lind L;Groop L;Laakso M;Collins FS;Jukema JW;Palmer CNA;Grallert H;Metspalu A;Dehghan A;Köttgen A;Abecasis GR;Meigs JB;Rotter JI;Marchini J;Pedersen O;Hansen T;Langenberg C;Wareham NJ;Stefansson K;Gloyn AL;Morris AP;Boehnke M;McCarthy MI
通讯作者：
McCarthy MI
影响因子：
30.8
作者：
Bulik-Sullivan, Brendan K.;Loh, Po-Ru;Finucane, Hilary K.;Ripke, Stephan;Yang, Jian;Patterson, Nick;Daly, Mark J.;Price, Alkes L.;Neale, Benjamin M.
通讯作者：
Neale, Benjamin M.
影响因子：
30.8
作者：
Finucane HK;Bulik-Sullivan B;Gusev A;Trynka G;Reshef Y;Loh PR;Anttila V;Xu H;Zang C;Farh K;Ripke S;Day FR;ReproGen Consortium;Schizophrenia Working Group of the Psychiatric Genomics Consortium;RACI Consortium;Purcell S;Stahl E;Lindstrom S;Perry JR;Okada Y;Raychaudhuri S;Daly MJ;Patterson N;Neale BM;Price AL
通讯作者：
Price AL