Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels
Malena Erbe,Ben J. Hayes,Ben J. Hayes,Lakshmi K. Matukumalli,S. Goswami,Phil J. Bowman,Coralie M. Reich,B.A. Mason,Michael E. Goddard +8 more
TLDR
This work assessed the gain in accuracy of GEBV in Jersey cattle as a result of using a combined Holstein and Jersey reference population, with either 39,745 or 624,213 single nucleotide polymorphism (SNP) markers.About:
This article is published in Journal of Dairy Science.The article was published on 2012-07-01 and is currently open access. It has received 551 citations till now. The article focuses on the topics: Population.read more
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Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores
Bjarni J. Vilhjálmsson,Jian Yang,Hilary K. Finucane,Alexander Gusev,Sara Lindström,Stephan Ripke,Giulio Genovese,Po-Ru Loh,Gaurav Bhatia,Ron Do,Tristan J. Hayeck,Hong-Hee Won,Benjamin M. Neale,Aiden Corvin,James T.R. Walters,Kai How Farh,Peter Holmans,Phil Lee,Brendan Bulik-Sullivan,David A. Collier,Hailiang Huang,Tune H. Pers,Ingrid Agartz,E. Agerbo,Margot Albus,Madeline Alexander,Farooq Amin,Silviu Alin 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 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,Nicholas John Craddock,James J. Crowley,David Curtis,Michael Davidson,Kenneth L. Davis,Franziska Degenhardt,Jurgen Del Favero,Lynn E. DeLisi,Ditte Demontis,Dimitris Dikeos,Timothy G. Dinan,Srdjan Djurovic,Gary Donohoe,Elodie Drapeau,Jubao Duan,Frank Dudbridge,Naser Durmishi,Peter Eichhammer,Johan G. 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 Henskens,Stefan Herms,Joel N. Hirschhorn,Per Hoffmann,A. Hofman,Mads V. Hollegaard,David M. Hougaard,Masashi Ikeda,Inge Joa,Antonio Julià,René S. Kahn,Luba Kalaydjieva,Sena Karachanak-Yankova,Juha Karjalainen,David J. Kavanagh,Matthew C. Keller,Brian Kelly,James L. Kennedy,Andrey Khrunin,Yunjung Kim,Janis Klovins,James A. Knowles,Bettina Konte,Vaidutis Kučinskas,Zita Ausrele Kucinskiene,Hana Kuzelova-Ptackova,Anna K. Kähler,Claudine Laurent,Jimmy Lee Chee Keong,S. Hong Lee,Sophie E. Legge,Bernard Lerer,Miaoxin Li,Tao Li,Kung Yee Liang,Jeffrey A. Lieberman,Svetlana A. Limborska,Carmel M. Loughland,Jan Lubinski,Jouko K. 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,Béla Melegh,Ingrid Melle,Raquelle I. Mesholam-Gately,Andres Metspalu,Patricia T. Michie,Lili Milani,Vihra Milanova,Younes Mokrab,Derek W. Morris,Ole Mors,Preben Bo 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 Pocklington,John Powell,Alkes Price,Ann E. Pulver,Shaun Purcell,Digby Quested,Henrik B. Rasmussen,Abraham Reichenberg,Mark Reimers,Alexander Richards,Joshua L. Roffman,Panos Roussos,Douglas M. Ruderfer,Veikko Salomaa,Alan R. Sanders,Ulrich Schall,Christian 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 Stögmann,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 L. Waddington,Dermot Walsh,Dai Wang,Qiang Wang,Bradley T. Webb,Mark Weiser,Dieter B. Wildenauer,Nigel Williams,Stephanie Williams,Stephanie H. Witt,Aaron R. Wolen,Emily H. M. Wong,Brandon Wormley,Jing Qin Wu,Hualin Simon Xi,Clement C. Zai,Xuebin Zheng,Fritz Zimprich,Naomi R. Wray,Kari Stefansson,Peter M. Visscher,Rolf Adolfsson,Ole A. Andreassen,Douglas Blackwood,Elvira Bramon,Joseph D. Buxbaum,Anders D. Børglum,Sven Cichon,Ariel Darvasi,Enrico Domenici,Hannelore Ehrenreich,Tõnu Esko,Pablo V. Gejman,Michael Gill,Hugh Gurling,Christina M. Hultman,Nakao Iwata,Assen Jablensky,Erik G. Jönsson,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 John Owen,A. 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 Conlon O'Donovan,Peter Kraft,David J. Hunter,Muriel A. Adank,Habibul Ahsan,Kristiina Aittomäki,Laura Baglietto,Sonja I. Berndt,Carl Blomquist,Federico Canzian,Jenny Chang-Claude,Stephen J. Chanock,Laura Crisponi,Kamila Czene,Norbert Dahmen,Isabel dos Santos Silva,Douglas F. Easton,A. Heather Eliassen,Jonine D. 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.M. Peeters,Julian Peto,Ross L. Prentice,Nazneen Rahman,María José Sánchez,Daniel F. Schmidt,Rita K. Schmutzler,Melissa C. Southey,Rulla M. Tamimi,Ruth C. Travis,Clare Turnbull,André G. Uitterlinden,Rob B. van der Luijt,Quinten Waisfisz,Zhaoming Wang,Alice S. Whittemore,Rose Yang,Wei Zheng,Wei Zheng,Sekar Kathiresan,Michele T. Pato,Carlos N. Pato,E Stahl,Noah Zaitlen,Bogdan Pasaniuc,Gillian M. Belbin,Eimear E. Kenny,Mikkel H. Schierup,Phillip L. De Jager,Nikolaos A. Patsopoulos,Steve McCarroll,Mark J. Daly,Shaun M. Purcell,Daniel I. Chasman,Benjamin M. Neale,Michael E. Goddard,Nick Patterson,Alkes L. Price +394 more
TL;DR: LDpred is introduced, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel, and outperforms the approach of pruning followed by thresholding, particularly at large sample sizes.
Journal ArticleDOI
Advantages and pitfalls in the application of mixed-model association methods
Jian Yang,Noah Zaitlen,Michael E. Goddard,Peter M. Visscher,Peter M. Visscher,Alkes L. Price +5 more
TL;DR: The advantages and pitfalls of MLMA methods as a function of study design are described and quantify and recommendations for the application of these methods in practical settings are provided.
Journal ArticleDOI
Polygenic modeling with bayesian sparse linear mixed models.
TL;DR: This work applies Bayesian sparse linear mixed model (BSLMM) and compares it with other methods for two polygenic modeling applications: estimating the proportion of variance in phenotypes explained (PVE) by available genotypes, and phenotype (or breeding value) prediction, and demonstrates that BSLMM considerably outperforms either of the other two methods.
Journal ArticleDOI
Polygenic prediction via Bayesian regression and continuous shrinkage priors.
Tian Ge,Tian Ge,Chia-Yen Chen,Yang Ni,Yen-Chen Anne Feng,Jordan W. Smoller,Jordan W. Smoller +6 more
TL;DR: Polygenic risk scores method PRS-CS is presented, a polygenic prediction method that infers posterior effect sizes of single nucleotide polymorphisms (SNPs) using genome-wide association summary statistics and an external linkage disequilibrium (LD) reference panel.
Journal ArticleDOI
Pitfalls of predicting complex traits from SNPs
Naomi R. Wray,Jian Yang,Ben J. Hayes,Ben J. Hayes,Alkes L. Price,Michael E. Goddard,Peter M. Visscher +6 more
TL;DR: Some of the limitations and pitfalls of prediction analysis are discussed and how naive implementations can lead to severe bias and misinterpretation of results are shown.
References
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Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
TL;DR: It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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Efficient Methods to Compute Genomic Predictions
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Common SNPs explain a large proportion of the heritability for human height
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