Literature DB >> 29522091

Beyond heritability: improving discoverability in imaging genetics.

Chun Chieh Fan1, Olav B Smeland2, Andrew J Schork3, Chi-Hua Chen1,4, Dominic Holland5, Min-Tzu Lo1,4, V S Sundar1,4, Oleksandr Frei2, Terry L Jernigan6, Ole A Andreassen2, Anders M Dale1,4,5.   

Abstract

Structural neuroimaging measures based on magnetic resonance imaging have been at the forefront of imaging genetics. Global efforts to ensure homogeneity of measurements across study sites have enabled large-scale imaging genetic projects, accumulating nearly 50K samples for genome-wide association studies (GWAS). However, not many novel genetic variants have been identified by these GWAS, despite the high heritability of structural neuroimaging measures. Here, we discuss the limitations of using heritability as a guidance for assessing statistical power of GWAS, and highlight the importance of discoverability-which is the power to detect genetic variants for a given phenotype depending on its unique genomic architecture and GWAS sample size. Further, we present newly developed methods that boost genetic discovery in imaging genetics. By redefining imaging measures independent of traditional anatomical conventions, it is possible to improve discoverability, enabling identification of more genetic effects. Moreover, by leveraging enrichment priors from genomic annotations and independent GWAS of pleiotropic traits, we can better characterize effect size distributions, and identify reliable and replicable loci associated with structural neuroimaging measures. Statistical tools leveraging novel insights into the genetic discoverability of human traits, promises to accelerate the identification of genetic underpinnings underlying brain structural variation.

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Year:  2018        PMID: 29522091      PMCID: PMC5946904          DOI: 10.1093/hmg/ddy082

Source DB:  PubMed          Journal:  Hum Mol Genet        ISSN: 0964-6906            Impact factor:   6.150


  61 in total

1.  Weighting sequence variants based on their annotation increases power of whole-genome association studies.

Authors:  Gardar Sveinbjornsson; Anders Albrechtsen; Florian Zink; Sigurjón A Gudjonsson; Asmundur Oddson; Gísli Másson; Hilma Holm; Augustine Kong; Unnur Thorsteinsdottir; Patrick Sulem; Daniel F Gudbjartsson; Kari Stefansson
Journal:  Nat Genet       Date:  2016-02-08       Impact factor: 38.330

2.  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

3.  Massively expedited genome-wide heritability analysis (MEGHA).

Authors:  Tian Ge; Thomas E Nichols; Phil H Lee; Avram J Holmes; Joshua L Roffman; Randy L Buckner; Mert R Sabuncu; Jordan W Smoller
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-09       Impact factor: 11.205

4.  Genetic Overlap Between Schizophrenia and Volumes of Hippocampus, Putamen, and Intracranial Volume Indicates Shared Molecular Genetic Mechanisms.

Authors:  Olav B Smeland; Yunpeng Wang; Oleksandr Frei; Wen Li; Derrek P Hibar; Barbara Franke; Francesco Bettella; Aree Witoelar; Srdjan Djurovic; Chi-Hua Chen; Paul M Thompson; Anders M Dale; Ole A Andreassen
Journal:  Schizophr Bull       Date:  2018-06-06       Impact factor: 9.306

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.  GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation.

Authors:  Qiongshi Lu; Xinwei Yao; Yiming Hu; Hongyu Zhao
Journal:  Bioinformatics       Date:  2015-10-25       Impact factor: 6.931

7.  A pleiotropy-informed Bayesian false discovery rate adapted to a shared control design finds new disease associations from GWAS summary statistics.

Authors:  James Liley; Chris Wallace
Journal:  PLoS Genet       Date:  2015-02-06       Impact factor: 5.917

8.  Large-scale genomics unveil polygenic architecture of human cortical surface area.

Authors:  Chi-Hua Chen; Qian Peng; Andrew J Schork; Min-Tzu Lo; Chun-Chieh Fan; Yunpeng Wang; Rahul S Desikan; Francesco Bettella; Donald J Hagler; Lars T Westlye; William S Kremen; Terry L Jernigan; Stephanie Le Hellard; Vidar M Steen; Thomas Espeseth; Matt Huentelman; Asta K Håberg; Ingrid Agartz; Srdjan Djurovic; Ole A Andreassen; Nicholas Schork; Anders M Dale
Journal:  Nat Commun       Date:  2015-07-20       Impact factor: 14.919

9.  Multimodal population brain imaging in the UK Biobank prospective epidemiological study.

Authors:  Karla L Miller; Fidel Alfaro-Almagro; Neal K Bangerter; David L Thomas; Essa Yacoub; Junqian Xu; Andreas J Bartsch; Saad Jbabdi; Stamatios N Sotiropoulos; Jesper L R Andersson; Ludovica Griffanti; Gwenaëlle Douaud; Thomas W Okell; Peter Weale; Iulius Dragonu; Steve Garratt; Sarah Hudson; Rory Collins; Mark Jenkinson; Paul M Matthews; Stephen M Smith
Journal:  Nat Neurosci       Date:  2016-09-19       Impact factor: 24.884

10.  Genome-wide association analysis identifies 13 new risk loci for schizophrenia.

Authors:  Stephan Ripke; Colm O'Dushlaine; Kimberly Chambert; Jennifer L Moran; Anna K Kähler; Susanne Akterin; Sarah E Bergen; Ann L Collins; James J Crowley; Menachem Fromer; Yunjung Kim; Sang Hong Lee; Patrik K E Magnusson; Nick Sanchez; Eli A Stahl; Stephanie Williams; Naomi R Wray; Kai Xia; Francesco Bettella; Anders D Borglum; Brendan K Bulik-Sullivan; Paul Cormican; Nick Craddock; Christiaan de Leeuw; Naser Durmishi; Michael Gill; Vera Golimbet; Marian L Hamshere; Peter Holmans; David M Hougaard; Kenneth S Kendler; Kuang Lin; Derek W Morris; Ole Mors; Preben B Mortensen; Benjamin M Neale; Francis A O'Neill; Michael J Owen; Milica Pejovic Milovancevic; Danielle Posthuma; John Powell; Alexander L Richards; Brien P Riley; Douglas Ruderfer; Dan Rujescu; Engilbert Sigurdsson; Teimuraz Silagadze; August B Smit; Hreinn Stefansson; Stacy Steinberg; Jaana Suvisaari; Sarah Tosato; Matthijs Verhage; James T Walters; Douglas F Levinson; Pablo V Gejman; Kenneth S Kendler; Claudine Laurent; Bryan J Mowry; Michael C O'Donovan; Michael J Owen; Ann E Pulver; Brien P Riley; Sibylle G Schwab; Dieter B Wildenauer; Frank Dudbridge; Peter Holmans; Jianxin Shi; Margot Albus; Madeline Alexander; Dominique Campion; David Cohen; Dimitris Dikeos; Jubao Duan; Peter Eichhammer; Stephanie Godard; Mark Hansen; F Bernard Lerer; Kung-Yee Liang; Wolfgang Maier; Jacques Mallet; Deborah A Nertney; Gerald Nestadt; Nadine Norton; Francis A O'Neill; George N Papadimitriou; Robert Ribble; Alan R Sanders; Jeremy M Silverman; Dermot Walsh; Nigel M Williams; Brandon Wormley; Maria J Arranz; Steven Bakker; Stephan Bender; Elvira Bramon; David Collier; Benedicto Crespo-Facorro; Jeremy Hall; Conrad Iyegbe; Assen Jablensky; Rene S Kahn; Luba Kalaydjieva; Stephen Lawrie; Cathryn M Lewis; Kuang Lin; Don H Linszen; Ignacio Mata; Andrew McIntosh; Robin M Murray; Roel A Ophoff; John Powell; Dan Rujescu; Jim Van Os; Muriel Walshe; Matthias Weisbrod; Durk Wiersma; Peter Donnelly; Ines Barroso; Jenefer M Blackwell; Elvira Bramon; Matthew A Brown; Juan P Casas; Aiden P Corvin; Panos Deloukas; Audrey Duncanson; Janusz Jankowski; Hugh S Markus; Christopher G Mathew; Colin N A Palmer; Robert Plomin; Anna Rautanen; Stephen J Sawcer; Richard C Trembath; Ananth C Viswanathan; Nicholas W Wood; Chris C A Spencer; Gavin Band; Céline Bellenguez; Colin Freeman; Garrett Hellenthal; Eleni Giannoulatou; Matti Pirinen; Richard D Pearson; Amy Strange; Zhan Su; Damjan Vukcevic; Peter Donnelly; Cordelia Langford; Sarah E Hunt; Sarah Edkins; Rhian Gwilliam; Hannah Blackburn; Suzannah J Bumpstead; Serge Dronov; Matthew Gillman; Emma Gray; Naomi Hammond; Alagurevathi Jayakumar; Owen T McCann; Jennifer Liddle; Simon C Potter; Radhi Ravindrarajah; Michelle Ricketts; Avazeh Tashakkori-Ghanbaria; Matthew J Waller; Paul Weston; Sara Widaa; Pamela Whittaker; Ines Barroso; Panos Deloukas; Christopher G Mathew; Jenefer M Blackwell; Matthew A Brown; Aiden P Corvin; Mark I McCarthy; Chris C A Spencer; Elvira Bramon; Aiden P Corvin; Michael C O'Donovan; Kari Stefansson; Edward Scolnick; Shaun Purcell; Steven A McCarroll; Pamela Sklar; Christina M Hultman; Patrick F Sullivan
Journal:  Nat Genet       Date:  2013-08-25       Impact factor: 38.330

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  5 in total

1.  Genetic Markers of ADHD-Related Variations in Intracranial Volume.

Authors:  Marieke Klein; Raymond K Walters; Ditte Demontis; Jason L Stein; Derrek P Hibar; Hieab H Adams; Janita Bralten; Nina Roth Mota; Russell Schachar; Edmund Sonuga-Barke; Manuel Mattheisen; Benjamin M Neale; Paul M Thompson; Sarah E Medland; Anders D Børglum; Stephen V Faraone; Alejandro Arias-Vasquez; Barbara Franke
Journal:  Am J Psychiatry       Date:  2019-03-01       Impact factor: 18.112

2.  Bivariate causal mixture model quantifies polygenic overlap between complex traits beyond genetic correlation.

Authors:  Oleksandr Frei; Dominic Holland; Olav B Smeland; Alexey A Shadrin; Chun Chieh Fan; Steffen Maeland; Kevin S O'Connell; Yunpeng Wang; Srdjan Djurovic; Wesley K Thompson; Ole A Andreassen; Anders M Dale
Journal:  Nat Commun       Date:  2019-06-03       Impact factor: 14.919

3.  Clinical opportunity awaits at the intersection of genomics and brain imaging.

Authors:  Carolina Makowski; Hao Wang; Chi-Hua Chen
Journal:  J Psychiatry Neurosci       Date:  2022-08-10       Impact factor: 5.699

4.  Identifying genetic markers enriched by brain imaging endophenotypes in Alzheimer's disease.

Authors:  Mansu Kim; Ruiming Wu; Xiaohui Yao; Andrew J Saykin; Jason H Moore; Li Shen
Journal:  BMC Med Genomics       Date:  2022-08-01       Impact factor: 3.622

5.  Quantifying the Polygenic Architecture of the Human Cerebral Cortex: Extensive Genetic Overlap between Cortical Thickness and Surface Area.

Authors:  Dennis van der Meer; Oleksandr Frei; Tobias Kaufmann; Chi-Hua Chen; Wesley K Thompson; Kevin S O'Connell; Jennifer Monereo Sánchez; David E J Linden; Lars T Westlye; Anders M Dale; Ole A Andreassen
Journal:  Cereb Cortex       Date:  2020-09-03       Impact factor: 5.357

  5 in total

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