Literature DB >> 25664543

Accurate liability estimation improves power in ascertained case-control studies.

Omer Weissbrod1, Christoph Lippert2, Dan Geiger1, David Heckerman2.   

Abstract

Linear mixed models (LMMs) have emerged as the method of choice for confounded genome-wide association studies. However, the performance of LMMs in nonrandomly ascertained case-control studies deteriorates with increasing sample size. We propose a framework called LEAP (liability estimator as a phenotype; https://github.com/omerwe/LEAP) that tests for association with estimated latent values corresponding to severity of phenotype, and we demonstrate that this can lead to a substantial power increase.

Mesh：

Year:  2015        PMID： 25664543     DOI： 10.1038/nmeth.3285

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  25 in total

1.  Improved linear mixed models for genome-wide association studies.

Authors:  Jennifer Listgarten; Christoph Lippert; Carl M Kadie; Robert I Davidson; Eleazar Eskin; David Heckerman
Journal:  Nat Methods       Date:  2012-05-30       Impact factor: 28.547

2.  Principal components analysis corrects for stratification in genome-wide association studies.

Authors:  Alkes L Price; Nick J Patterson; Robert M Plenge; Michael E Weinblatt; Nancy A Shadick; David Reich
Journal:  Nat Genet       Date:  2006-07-23       Impact factor: 38.330

3.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

Authors:  Lucia A Hindorff; Praveen Sethupathy; Heather A Junkins; Erin M Ramos; Jayashri P Mehta; Francis S Collins; Teri A Manolio
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-27       Impact factor: 11.205

4.  FaST linear mixed models for genome-wide association studies.

Authors:  Christoph Lippert; Jennifer Listgarten; Ying Liu; Carl M Kadie; Robert I Davidson; David Heckerman
Journal:  Nat Methods       Date:  2011-09-04       Impact factor: 28.547

5.  Common SNPs explain a large proportion of the heritability for human height.

Authors:  Jian Yang; Beben Benyamin; Brian P McEvoy; Scott Gordon; Anjali K Henders; Dale R Nyholt; Pamela A Madden; Andrew C Heath; Nicholas G Martin; Grant W Montgomery; Michael E Goddard; Peter M Visscher
Journal:  Nat Genet       Date:  2010-06-20       Impact factor: 38.330

6.  Advantages and pitfalls in the application of mixed-model association methods.

Authors:  Jian Yang; Noah A Zaitlen; Michael E Goddard; Peter M Visscher; Alkes L Price
Journal:  Nat Genet       Date:  2014-02       Impact factor: 38.330

7.  Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity.

Authors:  Lam C Tsoi; Sarah L Spain; Jo Knight; Eva Ellinghaus; Philip E Stuart; Francesca Capon; Jun Ding; Yanming Li; Trilokraj Tejasvi; Johann E Gudjonsson; Hyun M Kang; Michael H Allen; Ross McManus; Giuseppe Novelli; Lena Samuelsson; Joost Schalkwijk; Mona Ståhle; A David Burden; Catherine H Smith; Michael J Cork; Xavier Estivill; Anne M Bowcock; Gerald G Krueger; Wolfgang Weger; Jane Worthington; Rachid Tazi-Ahnini; Frank O Nestle; Adrian Hayday; Per Hoffmann; Juliane Winkelmann; Cisca Wijmenga; Cordelia Langford; Sarah Edkins; Robert Andrews; Hannah Blackburn; Amy Strange; Gavin Band; Richard D Pearson; Damjan Vukcevic; Chris C A Spencer; Panos Deloukas; Ulrich Mrowietz; Stefan Schreiber; Stephan Weidinger; Sulev Koks; Külli Kingo; Tonu Esko; Andres Metspalu; Henry W Lim; John J Voorhees; Michael Weichenthal; H Erich Wichmann; Vinod Chandran; Cheryl F Rosen; Proton Rahman; Dafna D Gladman; Christopher E M Griffiths; Andre Reis; Juha Kere; Rajan P Nair; Andre Franke; Jonathan N W N Barker; Goncalo R Abecasis; James T Elder; Richard C Trembath
Journal:  Nat Genet       Date:  2012-11-11       Impact factor: 38.330

8.  Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Authors:  Stephen Sawcer; Garrett Hellenthal; Matti Pirinen; Chris C A Spencer; Nikolaos A Patsopoulos; Loukas Moutsianas; Alexander Dilthey; Zhan Su; Colin Freeman; Sarah E Hunt; Sarah Edkins; Emma Gray; David R Booth; Simon C Potter; An Goris; Gavin Band; Annette Bang Oturai; Amy Strange; Janna Saarela; Céline Bellenguez; Bertrand Fontaine; Matthew Gillman; Bernhard Hemmer; Rhian Gwilliam; Frauke Zipp; Alagurevathi Jayakumar; Roland Martin; Stephen Leslie; Stanley Hawkins; Eleni Giannoulatou; Sandra D'alfonso; Hannah Blackburn; Filippo Martinelli Boneschi; Jennifer Liddle; Hanne F Harbo; Marc L Perez; Anne Spurkland; Matthew J Waller; Marcin P Mycko; Michelle Ricketts; Manuel Comabella; Naomi Hammond; Ingrid Kockum; Owen T McCann; Maria Ban; Pamela Whittaker; Anu Kemppinen; Paul Weston; Clive Hawkins; Sara Widaa; John Zajicek; Serge Dronov; Neil Robertson; Suzannah J Bumpstead; Lisa F Barcellos; Rathi Ravindrarajah; Roby Abraham; Lars Alfredsson; Kristin Ardlie; Cristin Aubin; Amie Baker; Katharine Baker; Sergio E Baranzini; Laura Bergamaschi; Roberto Bergamaschi; Allan Bernstein; Achim Berthele; Mike Boggild; Jonathan P Bradfield; David Brassat; Simon A Broadley; Dorothea Buck; Helmut Butzkueven; Ruggero Capra; William M Carroll; Paola Cavalla; Elisabeth G Celius; Sabine Cepok; Rosetta Chiavacci; Françoise Clerget-Darpoux; Katleen Clysters; Giancarlo Comi; Mark Cossburn; Isabelle Cournu-Rebeix; Mathew B Cox; Wendy Cozen; Bruce A C Cree; Anne H Cross; Daniele Cusi; Mark J Daly; Emma Davis; Paul I W de Bakker; Marc Debouverie; Marie Beatrice D'hooghe; Katherine Dixon; Rita Dobosi; Bénédicte Dubois; David Ellinghaus; Irina Elovaara; Federica Esposito; Claire Fontenille; Simon Foote; Andre Franke; Daniela Galimberti; Angelo Ghezzi; Joseph Glessner; Refujia Gomez; Olivier Gout; Colin Graham; Struan F A Grant; Franca Rosa Guerini; Hakon Hakonarson; Per Hall; Anders Hamsten; Hans-Peter Hartung; Rob N Heard; Simon Heath; Jeremy Hobart; Muna Hoshi; Carmen Infante-Duarte; Gillian Ingram; Wendy Ingram; Talat Islam; Maja Jagodic; Michael Kabesch; Allan G Kermode; Trevor J Kilpatrick; Cecilia Kim; Norman Klopp; Keijo Koivisto; Malin Larsson; Mark Lathrop; Jeannette S Lechner-Scott; Maurizio A Leone; Virpi Leppä; Ulrika Liljedahl; Izaura Lima Bomfim; Robin R Lincoln; Jenny Link; Jianjun Liu; Aslaug R Lorentzen; Sara Lupoli; Fabio Macciardi; Thomas Mack; Mark Marriott; Vittorio Martinelli; Deborah Mason; Jacob L McCauley; Frank Mentch; Inger-Lise Mero; Tania Mihalova; Xavier Montalban; John Mottershead; Kjell-Morten Myhr; Paola Naldi; William Ollier; Alison Page; Aarno Palotie; Jean Pelletier; Laura Piccio; Trevor Pickersgill; Fredrik Piehl; Susan Pobywajlo; Hong L Quach; Patricia P Ramsay; Mauri Reunanen; Richard Reynolds; John D Rioux; Mariaemma Rodegher; Sabine Roesner; Justin P Rubio; Ina-Maria Rückert; Marco Salvetti; Erika Salvi; Adam Santaniello; Catherine A Schaefer; Stefan Schreiber; Christian Schulze; Rodney J Scott; Finn Sellebjerg; Krzysztof W Selmaj; David Sexton; Ling Shen; Brigid Simms-Acuna; Sheila Skidmore; Patrick M A Sleiman; Cathrine Smestad; Per Soelberg Sørensen; Helle Bach Søndergaard; Jim Stankovich; Richard C Strange; Anna-Maija Sulonen; Emilie Sundqvist; Ann-Christine Syvänen; Francesca Taddeo; Bruce Taylor; Jenefer M Blackwell; Pentti Tienari; Elvira Bramon; Ayman Tourbah; Matthew A Brown; Ewa Tronczynska; Juan P Casas; Niall Tubridy; Aiden Corvin; Jane Vickery; Janusz Jankowski; Pablo Villoslada; Hugh S Markus; Kai Wang; Christopher G Mathew; James Wason; Colin N A Palmer; H-Erich Wichmann; Robert Plomin; Ernest Willoughby; Anna Rautanen; Juliane Winkelmann; Michael Wittig; Richard C Trembath; Jacqueline Yaouanq; Ananth C Viswanathan; Haitao Zhang; Nicholas W Wood; Rebecca Zuvich; Panos Deloukas; Cordelia Langford; Audrey Duncanson; Jorge R Oksenberg; Margaret A Pericak-Vance; Jonathan L Haines; Tomas Olsson; Jan Hillert; Adrian J Ivinson; Philip L De Jager; Leena Peltonen; Graeme J Stewart; David A Hafler; Stephen L Hauser; Gil McVean; Peter Donnelly; Alastair Compston
Journal:  Nature       Date:  2011-08-10       Impact factor: 49.962

9.  Population structure and eigenanalysis.

Authors:  Nick Patterson; Alkes L Price; David Reich
Journal:  PLoS Genet       Date:  2006-12       Impact factor: 5.917

10.  Further improvements to linear mixed models for genome-wide association studies.

Authors:  Christian Widmer; Christoph Lippert; Omer Weissbrod; Nicolo Fusi; Carl Kadie; Robert Davidson; Jennifer Listgarten; David Heckerman
Journal:  Sci Rep       Date:  2014-11-12       Impact factor: 4.379
View more
  20 in total

1.  Mixed Model Association with Family-Biased Case-Control Ascertainment.

Authors:  Tristan J Hayeck; Po-Ru Loh; Samuela Pollack; Alexander Gusev; Nick Patterson; Noah A Zaitlen; Alkes L Price
Journal:  Am J Hum Genet       Date:  2016-12-22       Impact factor: 11.025

2.  Control for Population Structure and Relatedness for Binary Traits in Genetic Association Studies via Logistic Mixed Models.

Authors:  Han Chen; Chaolong Wang; Matthew P Conomos; Adrienne M Stilp; Zilin Li; Tamar Sofer; Adam A Szpiro; Wei Chen; John M Brehm; Juan C Celedón; Susan Redline; George J Papanicolaou; Timothy A Thornton; Cathy C Laurie; Kenneth Rice; Xihong Lin
Journal:  Am J Hum Genet       Date:  2016-03-24       Impact factor: 11.025

Review 3.  Retrospective Association Analysis of Binary Traits: Overcoming Some Limitations of the Additive Polygenic Model.

Authors:  Duo Jiang; Joelle Mbatchou; Mary Sara McPeek
Journal:  Hum Hered       Date:  2016-09-01       Impact factor: 0.444

4.  Multi-scale inference of genetic trait architecture using biologically annotated neural networks.

Authors:  Pinar Demetci; Wei Cheng; Gregory Darnell; Xiang Zhou; Sohini Ramachandran; Lorin Crawford
Journal:  PLoS Genet       Date:  2021-08-19       Impact factor: 5.917

5.  Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits.

Authors:  Wei Cheng; Sohini Ramachandran; Lorin Crawford
Journal:  PLoS Genet       Date:  2020-06-15       Impact factor: 5.917

6.  Transformation of Summary Statistics from Linear Mixed Model Association on All-or-None Traits to Odds Ratio.

Authors:  Luke R Lloyd-Jones; Matthew R Robinson; Jian Yang; Peter M Visscher
Journal:  Genetics       Date:  2018-02-02       Impact factor: 4.562

7.  Case-control association mapping by proxy using family history of disease.

Authors:  Jimmy Z Liu; Yaniv Erlich; Joseph K Pickrell
Journal:  Nat Genet       Date:  2017-01-16       Impact factor: 38.330

8.  Genetic Mechanisms Leading to Sex Differences Across Common Diseases and Anthropometric Traits.

Authors:  Michela Traglia; Dina Bseiso; Alexander Gusev; Brigid Adviento; Daniel S Park; Joel A Mefford; Noah Zaitlen; Lauren A Weiss
Journal:  Genetics       Date:  2016-12-14       Impact factor: 4.562

9.  Retrospective Binary-Trait Association Test Elucidates Genetic Architecture of Crohn Disease.

Authors:  Duo Jiang; Sheng Zhong; Mary Sara McPeek
Journal:  Am J Hum Genet       Date:  2016-01-28       Impact factor: 11.025

10.  A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests.

Authors:  Julian Hecker; F William Townes; Priyadarshini Kachroo; Cecelia Laurie; Jessica Lasky-Su; John Ziniti; Michael H Cho; Scott T Weiss; Nan M Laird; Christoph Lange
Journal:  Bioinformatics       Date:  2020-12-26       Impact factor: 6.937
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.