Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

Autor: Bjarni J. Vilhjálmsson, Jian Yang, Hilary K. Finucane, Alexander Gusev, Sara Lindström, Stephan Ripke, Giulio Genovese, Po-Ru Loh, Gaurav Bhatia, Ron Do, Tristan Hayeck, Hong-Hee Won, Sekar Kathiresan, Michele Pato, Carlos Pato, Rulla Tamimi, Eli Stahl, Noah Zaitlen, Bogdan Pasaniuc, Gillian Belbin, Eimear E. Kenny, Mikkel H. Schierup, Philip De Jager, Nikolaos A. Patsopoulos, Steve McCarroll, Mark Daly, Shaun Purcell, Daniel Chasman, Benjamin Neale, Michael Goddard, Peter M. Visscher, Peter Kraft, Nick Patterson, Alkes L. Price, Benjamin M. Neale, Aiden Corvin, James T.R. Walters, Kai-How Farh, Peter A. Holmans, Phil Lee, Brendan Bulik-Sullivan, David A. Collier, Hailiang Huang, Tune H. Pers, Ingrid Agartz, Esben Agerbo, Margot Albus, Madeline Alexander, Farooq Amin, Silviu A. Bacanu, Martin Begemann, Richard A. Belliveau, Judit Bene, Sarah E. Bergen, Elizabeth Bevilacqua, Tim B. Bigdeli, Donald W. Black, Richard Bruggeman, Nancy G. Buccola, Randy L. Buckner, William Byerley, Wiepke Cahn, Guiqing Cai, Dominique Campion, Rita M. Cantor, Vaughan J. Carr, Noa Carrera, Stanley V. Catts, Kimberly D. Chambert, Raymond C.K. Chan, Ronald Y.L. Chen, Eric Y.H. Chen, Wei Cheng, Eric F.C. Cheung, Siow Ann Chong, C. Robert Cloninger, David Cohen, Nadine Cohen, Paul Cormican, Nick Craddock, James J. Crowley, David Curtis, Michael Davidson, Kenneth L. Davis, Franziska Degenhardt, Jurgen Del Favero, Lynn E. DeLisi, Ditte Demontis, Dimitris Dikeos, Timothy Dinan, Srdjan Djurovic, Gary Donohoe, Elodie Drapeau, Jubao Duan, Frank Dudbridge, Naser Durmishi, Peter Eichhammer, Johan Eriksson, Valentina Escott-Price, Laurent Essioux, Ayman H. Fanous, Martilias S. Farrell, Josef Frank, Lude Franke, Robert Freedman, Nelson B. Freimer, Marion Friedl, Joseph I. Friedman, Menachem Fromer, Lyudmila Georgieva, Elliot S. Gershon, Ina Giegling, Paola Giusti-Rodrguez, Stephanie Godard, Jacqueline I. Goldstein, Vera Golimbet, Srihari Gopal, Jacob Gratten, Jakob Grove, Lieuwe de Haan, Christian Hammer, Marian L. Hamshere, Mark Hansen, Thomas Hansen, Vahram Haroutunian, Annette M. Hartmann, Frans A. Henskens, Stefan Herms, Joel N. Hirschhorn, Per Hoffmann, Andrea Hofman, Mads V. Hollegaard, David M. Hougaard, Masashi Ikeda, Inge Joa, Antonio Julia, Rene S. Kahn, Luba Kalaydjieva, Sena Karachanak-Yankova, Juha Karjalainen, David Kavanagh, Matthew C. Keller, Brian J. Kelly, James L. Kennedy, Andrey Khrunin, Yunjung Kim, Janis Klovins, James A. Knowles, Bettina Konte, Vaidutis Kucinskas, Zita Ausrele Kucinskiene, Hana Kuzelova-Ptackova, Anna K. Kahler, Claudine Laurent, Jimmy Lee Chee Keong, S. Hong Lee, Sophie E. Legge, Bernard Lerer, Miaoxin Li, Tao Li, Kung-Yee Liang, Jeffrey Lieberman, Svetlana Limborska, Carmel M. Loughland, Jan Lubinski, Jouko Lnnqvist, Milan Macek, Patrik K.E. Magnusson, Brion S. Maher, Wolfgang Maier, Jacques Mallet, Sara Marsal, Manuel Mattheisen, Morten Mattingsdal, Robert W. McCarley, Colm McDonald, Andrew M. McIntosh, Sandra Meier, Carin J. Meijer, Bela Melegh, Ingrid Melle, Raquelle I. Mesholam-Gately, Andres Metspalu, Patricia T. Michie, Lili Milani, Vihra Milanova, Younes Mokrab, Derek W. Morris, Ole Mors, Preben B. Mortensen, Kieran C. Murphy, Robin M. Murray, Inez Myin-Germeys, Bertram Mller-Myhsok, Mari Nelis, Igor Nenadic, Deborah A. Nertney, Gerald Nestadt, Kristin K. Nicodemus, Liene Nikitina-Zake, Laura Nisenbaum, Annelie Nordin, Eadbhard O’Callaghan, Colm O’Dushlaine, F. Anthony O’Neill, Sang-Yun Oh, Ann Olincy, Line Olsen, Jim Van Os, Christos Pantelis, George N. Papadimitriou, Sergi Papiol, Elena Parkhomenko, Michele T. Pato, Tiina Paunio, Milica Pejovic-Milovancevic, Diana O. Perkins, Olli Pietilinen, Jonathan Pimm, Andrew J. Pocklington, John Powell, Alkes Price, Ann E. Pulver, Shaun M. Purcell, Digby Quested, Henrik B. Rasmussen, Abraham Reichenberg, Mark A. Reimers, Alexander L. Richards, Joshua L. Roffman, Panos Roussos, Douglas M. Ruderfer, Veikko Salomaa, Alan R. Sanders, Ulrich Schall, Christian R. Schubert, Thomas G. Schulze, Sibylle G. Schwab, Edward M. Scolnick, Rodney J. Scott, Larry J. Seidman, Jianxin Shi, Engilbert Sigurdsson, Teimuraz Silagadze, Jeremy M. Silverman, Kang Sim, Petr Slominsky, Jordan W. Smoller, Hon-Cheong So, Chris C.A. Spencer, Eli A. Stahl, Hreinn Stefansson, Stacy Steinberg, Elisabeth Stogmann, Richard E. Straub, Eric Strengman, Jana Strohmaier, T. Scott Stroup, Mythily Subramaniam, Jaana Suvisaari, Dragan M. Svrakic, Jin P. Szatkiewicz, Erik Sderman, Srinivas Thirumalai, Draga Toncheva, Paul A. Tooney, Sarah Tosato, Juha Veijola, John Waddington, Dermot Walsh, Dai Wang, Qiang Wang, Bradley T. Webb, Mark Weiser, Dieter B. Wildenauer, Nigel M. Williams, Stephanie Williams, Stephanie H. Witt, Aaron R. Wolen, Emily H.M. Wong, Brandon K. Wormley, Jing Qin Wu, Hualin Simon Xi, Clement C. Zai, Xuebin Zheng, Fritz Zimprich, Naomi R. Wray, Kari Stefansson, Rolf Adolfsson, Ole A. Andreassen, Douglas H.R. Blackwood, Elvira Bramon, Joseph D. Buxbaum, Anders D. Børglum, Sven Cichon, Ariel Darvasi, Enrico Domenici, Hannelore Ehrenreich, Tonu Esko, Pablo V. Gejman, Michael Gill, Hugh Gurling, Christina M. Hultman, Nakao Iwata, Assen V. Jablensky, Erik G. Jonsson, Kenneth S. Kendler, George Kirov, Jo Knight, Todd Lencz, Douglas F. Levinson, Qingqin S. Li, Jianjun Liu, Anil K. Malhotra, Steven A. McCarroll, Andrew McQuillin, Jennifer L. Moran, Bryan J. Mowry, Markus M. Nthen, Roel A. Ophoff, Michael J. Owen, Aarno Palotie, Carlos N. Pato, Tracey L. Petryshen, Danielle Posthuma, Marcella Rietschel, Brien P. Riley, Dan Rujescu, Pak C. Sham, Pamela Sklar, David St. Clair, Daniel R. Weinberger, Jens R. Wendland, Thomas Werge, Mark J. Daly, Patrick F. Sullivan, Michael C. O’Donovan, David J. Hunter, Muriel Adank, Habibul Ahsan, Kristiina Aittomäki, Laura Baglietto, Sonja Berndt, Carl Blomquist, Federico Canzian, Jenny Chang-Claude, Stephen J. Chanock, Laura Crisponi, Kamila Czene, Norbert Dahmen, Isabel dos Santos Silva, Douglas Easton, A. Heather Eliassen, Jonine Figueroa, Olivia Fletcher, Montserrat Garcia-Closas, Mia M. Gaudet, Lorna Gibson, Christopher A. Haiman, Per Hall, Aditi Hazra, Rebecca Hein, Brian E. Henderson, Albert Hofman, John L. Hopper, Astrid Irwanto, Mattias Johansson, Rudolf Kaaks, Muhammad G. Kibriya, Peter Lichtner, Eiliv Lund, Enes Makalic, Alfons Meindl, Hanne Meijers-Heijboer, Bertram Müller-Myhsok, Taru A. Muranen, Heli Nevanlinna, Petra H. Peeters, Julian Peto, Ross L. Prentice, Nazneen Rahman, María José Sánchez, Daniel F. Schmidt, Rita K. Schmutzler, Melissa C. Southey, Ruth Travis, Clare Turnbull, Andre G. Uitterlinden, Rob B. van der Luijt, Quinten Waisfisz, Zhaoming Wang, Alice S. Whittemore, Rose Yang, Wei Zheng

Publikováno v: American journal of human genetics, 97(4), 576-592. Cell Press
Vilhjálmsson, B J, Yang, J, Finucane, H K, Gusev, A, Lindström, S, Ripke, S, Genovese, G, Loh, P-R, Bhatia, G, Do, R, Hayeck, T, Won, H-H, Kathiresan, S, Pato, M, Pato, C, Tamimi, R, Stahl, E, Zaitlen, N, Pasaniuc, B, Belbin, G, Kenny, E E, Schierup, M H, De Jager, P, Patsopoulos, N A, McCarroll, S, Daly, M, Purcell, S, Chasman, D, Neale, B, Goddard, M, Visscher, P M, Kraft, P, Patterson, N, Price, A L, Schizophrenia Working Group of the Psychiatric Genomics Consortium (Jakob Grove, member), Grove, J (ed.), Schizophrenia Working Group of the Psychiatric Genomics Consortium (Anders Børglum, member of-) & Børglum, A 2015, ' Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores ', American Journal of Human Genetics, vol. 97, no. 4, pp. 576-92 . https://doi.org/10.1016/j.ajhg.2015.09.001
Vilhjálmsson, B J, Yang, J, Finucane, H K, Gusev, A, Lindström, S, Ripke, S, Genovese, G, Loh, P R, Bhatia, G, Do, R, Hayeck, T, Won, H H, Neale, B, Corvin, A, Walters, J T R, Farh, K H, Holmans, P A, Lee, P, Bulik-Sullivan, B, Collier, D A, Huang, H, Pers, T H, Agartz, I, Agerbo, E, Albus, M, Alexander, M, Amin, F, Bacanu, S A, Begemann, M, Belliveau, R A, Bene, J, Bergen, S E, Bevilacqua, E, Bigdeli, T B, Black, D W, Bruggeman, R, Buccola, N G, Buckner, R L, Byerley, W, Cahn, W, Cai, G, Campion, D, Cantor, R M, Carr, V J, Carrera, N, Catts, S V, Chambert, K D, Chan, R C K, Chen, R Y L, Chen, E Y H, Cheng, W, Cheung, E F C, Chong, S A, Cloninger, C R, Cohen, D, Cohen, N, Cormican, P, Craddock, N, Crowley, J J, Curtis, D, Davidson, M, Davis, K L, Degenhardt, F, Del Favero, J, Delisi, L E, Demontis, D, Dikeos, D, Dinan, T, Djurovic, S, Donohoe, G, Drapeau, E, Duan, J, Dudbridge, F, Durmishi, N, Eichhammer, P, Eriksson, J, Escott-Price, V, Essioux, L, Fanous, A H, Farrell, M S, Frank, J, Franke, L, Freedman, R, Freimer, N B, Friedl, M, Friedman, J I, Fromer, M, Georgieva, L, Gershon, E S, Giegling, I, Giusti-Rodrguez, P, Godard, S, Goldstein, J I, Golimbet, V, Gopal, S, Gratten, J, Grove, J, De Haan, L, Hammer, C, Hamshere, M L, Hansen, M, Hansen, T, Haroutunian, V, Hartmann, A M, Henskens, F A, Herms, S, Hirschhorn, J N, Hoffmann, P, Hofman, A, Hollegaard, M V, Hougaard, D M, Ikeda, M, Joa, I, Julia, A, Kahn, R S, Kalaydjieva, L, Karachanak-Yankova, S, Karjalainen, J, Kavanagh, D, Keller, M C, Kelly, B J, Kennedy, J L, Khrunin, A, Kim, Y, Klovins, J, Knowles, J A, Konte, B, Kucinskas, V, Kucinskiene, Z A, Kuzelova-Ptackova, H, Kahler, A K, Laurent, C, Keong, J L C, Lee, S H, Legge, S E, Lerer, B, Li, M, Li, T, Liang, K Y, Lieberman, J, Limborska, S, Loughland, C M, Lubinski, J, Lnnqvist, J, Macek, M, Magnusson, P K E, Maher, B S, Maier, W, Mallet, J, Marsal, S, Mattheisen, M, Mattingsdal, M, McCarley, R W, McDonald, C, McIntosh, A M, Meier, S, Meijer, C J, Melegh, B, Melle, I, Mesholam-Gately, R I, Metspalu, A, Michie, P T, Milani, L, Milanova, V, Mokrab, Y, Morris, D W, Mors, O, Mortensen, P B, Murphy, K C, Murray, R M, Myin-Germeys, I, Mller-Myhsok, B, Nelis, M, Nenadic, I, Nertney, D A, Nestadt, G, Nicodemus, K K, Nikitina-Zake, L, Nisenbaum, L, Nordin, A, O'Callaghan, E, O'Dushlaine, C, O'Neill, F A, Oh, S Y, Olincy, A, Olsen, L, Van Os, J, Pantelis, C, Papadimitriou, G N, Papiol, S, Parkhomenko, E, Pato, M T, Paunio, T, Pejovic-Milovancevic, M, Perkins, D O, Pietilinen, O, Pimm, J, Pocklington, A J, Powell, J, Price, A, Pulver, A E, Purcell, S, Quested, D, Rasmussen, H B, Reichenberg, A, Reimers, M A, Richards, A L, Roffman, J L, Roussos, P, Ruderfer, D M, Salomaa, V, Sanders, A R, Schall, U, Schubert, C R, Schulze, T G, Schwab, S G, Scolnick, E M, Scott, R J, Seidman, L J, Shi, J, Sigurdsson, E, Silagadze, T, Silverman, J M, Sim, K, Slominsky, P, Smoller, J W, So, H C, Spencer, C C A, Stahl, E A, Stefansson, H, Steinberg, S, Stogmann, E, Straub, R E, Strengman, E, Strohmaier, J, Stroup, T S, Subramaniam, M, Suvisaari, J, Svrakic, D M, Szatkiewicz, J P, Sderman, E, Thirumalai, S, Toncheva, D, Tooney, P A, Tosato, S, Veijola, J, Waddington, J, Walsh, D, Wang, D, Wang, Q, Webb, B T, Weiser, M, Wildenauer, D B, Williams, N M, Williams, S, Witt, S H, Wolen, A R, Wong, E H M, Wormley, B K, Wu, J Q, Xi, H S, Zai, C C, Zheng, X, Zimprich, F, Wray, N R, Stefansson, K, Adolfsson, R, Andreassen, O A, Visscher, P M, Blackwood, D H R, Bramon, E, Buxbaum, J D, Børglum, A D, Cichon, S, Darvasi, A, Domenici, E, Ehrenreich, H, Esko, T, Gejman, P V, Gill, M, Gurling, H, Hultman, C M, Iwata, N, Jablensky, A V, Jonsson, E G, Kendler, K S, Kirov, G, Knight, J, Lencz, T, Levinson, D F, Li, Q S, Liu, J, Malhotra, A K, McCarroll, S A, McQuillin, A, Moran, J L, Mowry, B J, Nthen, M M, Ophoff, R A, Owen, M J, Palotie, A, Pato, C N, Petryshen, T L, Posthuma, D, Rietschel, M, Riley, B P, Rujescu, D, Sham, P C, Sklar, P, St. Clair, D, Weinberger, D R, Wendland, J R, Werge, T, Daly, M J, Sullivan, P F, O'Donovan, M C, Kraft, P, Hunter, D J, Adank, M, Ahsan, H, Aittomäki, K, Baglietto, L, Berndt, S, Blomquist, C, Canzian, F, Chang-Claude, J, Chanock, S J, Crisponi, L, Czene, K, Dahmen, N, Dos Santos Silva, I, Easton, D, Eliassen, A H, Figueroa, J, Fletcher, O, Garcia-Closas, M, Gaudet, M M, Gibson, L, Haiman, C A, Hall, P, Hazra, A, Hein, R, Henderson, B E, Hopper, J L, Irwanto, A, Johansson, M, Kaaks, R, Kibriya, M G, Lichtner, P, Lund, E, Makalic, E, Meindl, A, Meijers-Heijboer, H, Müller-Myhsok, B, Muranen, T A, Nevanlinna, H, Peeters, P H, Peto, J, Prentice, R L, Rahman, N, Sánchez, M J, Schmidt, D F, Schmutzler, R K, Southey, M C, Tamimi, R, Travis, R, Turnbull, C, Uitterlinden, A G, Van Der Luijt, R B, Waisfisz, Q, Wang, Z, Whittemore, A S, Yang, R, Zheng, W, Kathiresan, S, Pato, M, Pato, C, Stahl, E, Zaitlen, N, Pasaniuc, B, Kenny, E E, Schierup, M H, De Jager, P, Patsopoulos, N A, McCarroll, S, Daly, M, Purcell, S, Belbin, G, Neale, B, Goddard, M, Patterson, N, Price, A L, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Psychosis Endophenotypes International Consortium, Wellcome Trust Case-Control Consortium, Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) study & Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON) 2015, ' Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores ', American journal of human genetics, vol. 97, no. 4, pp. 576-592 . https://doi.org/10.1016/j.ajhg.2015.09.001
American Journal of Human Genetics, 97, 576-592. Cell Press
American Journal of Human Genetics
Vilhjálmsson, B J, Yang, J, Finucane, H K, Gusev, A, Lindström, S, Ripke, S, Genovese, G, Loh, P R, Bhatia, G, Do, R, Hayeck, T, Won, H H, Posthuma, D, Kathiresan, S, Pato, M, Pato, C, Tamimi, R, Stahl, E, Zaitlen, N, Pasaniuc, B, Belbin, G, Kenny, E E, Schierup, M H, De Jager, P, Patsopoulos, N A, McCarroll, S, Daly, M, Purcell, S, Chasman, D, Neale, B, Goddard, M, Visscher, P M, Kraft, P, Patterson, N & Price, A L 2015, ' Modeling linkage disequilibrium increases accuracy of polygenic risk scores ', American Journal of Human Genetics, vol. 97, pp. 576-592 . https://doi.org/10.1016/j.ajhg.2015.09.001
American Journal of Human Genetics, 97(4), 576-592. Cell Press
American journal of human genetics, vol 97, iss 4

Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pru

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