Literature DB >> 29726908

VarExp: estimating variance explained by genome-wide GxE summary statistics.

Vincent Laville1, Amy R Bentley2, Florian Privé1,3, Xiaofeng Zhu4, Jim Gauderman5, Thomas W Winkler6, Mike Province7, D C Rao8, Hugues Aschard1.   

Abstract

Summary: Many genome-wide association studies and genome-wide screening for gene-environment (GxE) interactions have been performed to elucidate the underlying mechanisms of human traits and diseases. When the analyzed outcome is quantitative, the overall contribution of identified genetic variants to the outcome is often expressed as the percentage of phenotypic variance explained. This is commonly done using individual-level genotype data but it is challenging when results are derived through meta-analyses. Here, we present R package, 'VarExp', that allows for the estimation of the percentage of phenotypic variance explained using summary statistics only. It allows for a range of models to be evaluated, including marginal genetic effects, GxE interaction effects and both effects jointly. Its implementation integrates all recent methodological developments and does not need external data to be uploaded by users. Availability and implementation: The R package is available at https://gitlab.pasteur.fr/statistical-genetics/VarExp.git. Supplementary information: Supplementary data are available at Bioinformatics online.

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Mesh：

Year:  2018        PMID： 29726908      PMCID： PMC6157079          DOI： 10.1093/bioinformatics/bty379

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  6 in total

1.  Genotype-covariate interaction effects and the heritability of adult body mass index.

Authors:  Matthew R Robinson; Geoffrey English; Gerhard Moser; Luke R Lloyd-Jones; Marcus A Triplett; Zhihong Zhu; Ilja M Nolte; Jana V van Vliet-Ostaptchouk; Harold Snieder; Tonu Esko; Lili Milani; Reedik Mägi; Andres Metspalu; Patrik K E Magnusson; Nancy L Pedersen; Erik Ingelsson; Magnus Johannesson; Jian Yang; David Cesarini; Peter M Visscher
Journal:  Nat Genet       Date:  2017-07-10       Impact factor: 38.330

2.  Contrasting the Genetic Architecture of 30 Complex Traits from Summary Association Data.

Authors:  Huwenbo Shi; Gleb Kichaev; Bogdan Pasaniuc
Journal:  Am J Hum Genet       Date:  2016-06-23       Impact factor: 11.025

Review 3.  Challenges and opportunities in genome-wide environmental interaction (GWEI) studies.

Authors:  Hugues Aschard; Sharon Lutz; Bärbel Maus; Eric J Duell; Tasha E Fingerlin; Nilanjan Chatterjee; Peter Kraft; Kristel Van Steen
Journal:  Hum Genet       Date:  2012-07-04       Impact factor: 4.132

4.  A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics.

Authors:  Guillaume Pare; Shihong Mao; Wei Q Deng
Journal:  Sci Rep       Date:  2016-06-08       Impact factor: 4.379

5.  A perspective on interaction effects in genetic association studies.

Authors:  Hugues Aschard
Journal:  Genet Epidemiol       Date:  2016-07-07       Impact factor: 2.135

6.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962
  6 in total
  7 in total

1.  Using Genetic Marginal Effects to Study Gene-Environment Interactions with GWAS Data.

Authors:  Brad Verhulst; Joshua N Pritikin; James Clifford; Elizabeth Prom-Wormley
Journal:  Behav Genet       Date:  2021-04-26       Impact factor: 2.805

2.  Multi-ancestry genome-wide gene-sleep interactions identify novel loci for blood pressure.

Authors:  Heming Wang; Raymond Noordam; Brian E Cade; Karen Schwander; Thomas W Winkler; Jiwon Lee; Yun Ju Sung; Amy R Bentley; Alisa K Manning; Hugues Aschard; Tuomas O Kilpeläinen; Marjan Ilkov; Michael R Brown; Andrea R Horimoto; Melissa Richard; Traci M Bartz; Dina Vojinovic; Elise Lim; Jovia L Nierenberg; Yongmei Liu; Kumaraswamynaidu Chitrala; Tuomo Rankinen; Solomon K Musani; Nora Franceschini; Rainer Rauramaa; Maris Alver; Phyllis C Zee; Sarah E Harris; Peter J van der Most; Ilja M Nolte; Patricia B Munroe; Nicholette D Palmer; Brigitte Kühnel; Stefan Weiss; Wanqing Wen; Kelly A Hall; Leo-Pekka Lyytikäinen; Jeff O'Connell; Gudny Eiriksdottir; Lenore J Launer; Paul S de Vries; Dan E Arking; Han Chen; Eric Boerwinkle; Jose E Krieger; Pamela J Schreiner; Stephen Sidney; James M Shikany; Kenneth Rice; Yii-Der Ida Chen; Sina A Gharib; Joshua C Bis; Annemarie I Luik; M Arfan Ikram; André G Uitterlinden; Najaf Amin; Hanfei Xu; Daniel Levy; Jiang He; Kurt K Lohman; Alan B Zonderman; Treva K Rice; Mario Sims; Gregory Wilson; Tamar Sofer; Stephen S Rich; Walter Palmas; Jie Yao; Xiuqing Guo; Jerome I Rotter; Nienke R Biermasz; Dennis O Mook-Kanamori; Lisa W Martin; Ana Barac; Robert B Wallace; Daniel J Gottlieb; Pirjo Komulainen; Sami Heikkinen; Reedik Mägi; Lili Milani; Andres Metspalu; John M Starr; Yuri Milaneschi; R J Waken; Chuan Gao; Melanie Waldenberger; Annette Peters; Konstantin Strauch; Thomas Meitinger; Till Roenneberg; Uwe Völker; Marcus Dörr; Xiao-Ou Shu; Sutapa Mukherjee; David R Hillman; Mika Kähönen; Lynne E Wagenknecht; Christian Gieger; Hans J Grabe; Wei Zheng; Lyle J Palmer; Terho Lehtimäki; Vilmundur Gudnason; Alanna C Morrison; Alexandre C Pereira; Myriam Fornage; Bruce M Psaty; Cornelia M van Duijn; Ching-Ti Liu; Tanika N Kelly; Michele K Evans; Claude Bouchard; Ervin R Fox; Charles Kooperberg; Xiaofeng Zhu; Timo A Lakka; Tõnu Esko; Kari E North; Ian J Deary; Harold Snieder; Brenda W J H Penninx; W James Gauderman; Dabeeru C Rao; Susan Redline; Diana van Heemst
Journal:  Mol Psychiatry       Date:  2021-04-15       Impact factor: 13.437

3.  Gene × Environment Interaction in Developmental Disorders: Where Do We Stand and What's Next?

Authors:  Gianluca Esposito; Atiqah Azhari; Jessica L Borelli
Journal:  Front Psychol       Date:  2018-10-26

4.  Multi-Ancestry Genome-wide Association Study Accounting for Gene-Psychosocial Factor Interactions Identifies Novel Loci for Blood Pressure Traits.

Authors:  Daokun Sun; Melissa Richard; Solomon K Musani; Yun Ju Sung; Thomas W Winkler; Karen Schwander; Jin Fang Chai; Xiuqing Guo; Tuomas O Kilpeläinen; Dina Vojinovic; Hugues Aschard; Traci M Bartz; Lawrence F Bielak; Michael R Brown; Kumaraswamy Chitrala; Fernando P Hartwig; Andrea R V R Horimoto; Yongmei Liu; Alisa K Manning; Raymond Noordam; Albert V Smith; Sarah E Harris; Brigitte Kühnel; Leo-Pekka Lyytikäinen; Ilja M Nolte; Rainer Rauramaa; Peter J van der Most; Rujia Wang; Erin B Ware; Stefan Weiss; Wanqing Wen; Lisa R Yanek; Dan E Arking; Donna K Arnett; Ana Barac; Eric Boerwinkle; Ulrich Broeckel; Aravinda Chakravarti; Yii-Der Ida Chen; L Adrienne Cupples; Martha L Davigulus; Lisa de Las Fuentes; Renée de Mutsert; Paul S de Vries; Joseph A C Delaney; Ana V Diez Roux; Marcus Dörr; Jessica D Faul; Amanda M Fretts; Linda C Gallo; Hans Jörgen Grabe; C Charles Gu; Tamara B Harris; Catharina C A Hartman; Sami Heikkinen; M Arfan Ikram; Carmen Isasi; W Craig Johnson; Jost Bruno Jonas; Robert C Kaplan; Pirjo Komulainen; Jose E Krieger; Daniel Levy; Jianjun Liu; Kurt Lohman; Annemarie I Luik; Lisa W Martin; Thomas Meitinger; Yuri Milaneschi; Jeff R O'Connell; Walter R Palmas; Annette Peters; Patricia A Peyser; Laura Pulkki-Råback; Leslie J Raffel; Alex P Reiner; Kenneth Rice; Jennifer G Robinson; Frits R Rosendaal; Carsten Oliver Schmidt; Pamela J Schreiner; Lars Schwettmann; James M Shikany; Xiao-Ou Shu; Stephen Sidney; Mario Sims; Jennifer A Smith; Nona Sotoodehnia; Konstantin Strauch; E Shyong Tai; Kent Taylor; André G Uitterlinden; Cornelia M van Duijn; Melanie Waldenberger; Hwee-Lin Wee; Wen-Bin Wei; Gregory Wilson; Deng Xuan; Jie Yao; Donglin Zeng; Wei Zhao; Xiaofeng Zhu; Alan B Zonderman; Diane M Becker; Ian J Deary; Christian Gieger; Timo A Lakka; Terho Lehtimäki; Kari E North; Albertine J Oldehinkel; Brenda W J H Penninx; Harold Snieder; Ya-Xing Wang; David R Weir; Wei Zheng; Michele K Evans; W James Gauderman; Vilmundur Gudnason; Bernardo L Horta; Ching-Ti Liu; Dennis O Mook-Kanamori; Alanna C Morrison; Alexandre C Pereira; Bruce M Psaty; Najaf Amin; Ervin R Fox; Charles Kooperberg; Xueling Sim; Laura Bierut; Jerome I Rotter; Sharon L R Kardia; Nora Franceschini; Dabeeru C Rao; Myriam Fornage
Journal:  HGG Adv       Date:  2020-10-31

5.  Gene-lifestyle interactions in the genomics of human complex traits.

Authors:  Vincent Laville; Timothy Majarian; Yun J Sung; Karen Schwander; Mary F Feitosa; Daniel I Chasman; Amy R Bentley; Charles N Rotimi; L Adrienne Cupples; Paul S de Vries; Michael R Brown; Alanna C Morrison; Aldi T Kraja; Mike Province; C Charles Gu; W James Gauderman; D C Rao; Alisa K Manning; Hugues Aschard
Journal:  Eur J Hum Genet       Date:  2022-03-22       Impact factor: 5.351

6.  Multi-ancestry sleep-by-SNP interaction analysis in 126,926 individuals reveals lipid loci stratified by sleep duration.

Authors:  Raymond Noordam; Maxime M Bos; Heming Wang; Thomas W Winkler; Amy R Bentley; Tuomas O Kilpeläinen; Paul S de Vries; Yun Ju Sung; Karen Schwander; Brian E Cade; Alisa Manning; Hugues Aschard; Michael R Brown; Han Chen; Nora Franceschini; Solomon K Musani; Melissa Richard; Dina Vojinovic; Stella Aslibekyan; Traci M Bartz; Lisa de Las Fuentes; Mary Feitosa; Andrea R Horimoto; Marjan Ilkov; Minjung Kho; Aldi Kraja; Changwei Li; Elise Lim; Yongmei Liu; Dennis O Mook-Kanamori; Tuomo Rankinen; Salman M Tajuddin; Ashley van der Spek; Zhe Wang; Jonathan Marten; Vincent Laville; Maris Alver; Evangelos Evangelou; Maria E Graff; Meian He; Brigitte Kühnel; Leo-Pekka Lyytikäinen; Pedro Marques-Vidal; Ilja M Nolte; Nicholette D Palmer; Rainer Rauramaa; Xiao-Ou Shu; Harold Snieder; Stefan Weiss; Wanqing Wen; Lisa R Yanek; Correa Adolfo; Christie Ballantyne; Larry Bielak; Nienke R Biermasz; Eric Boerwinkle; Niki Dimou; Gudny Eiriksdottir; Chuan Gao; Sina A Gharib; Daniel J Gottlieb; José Haba-Rubio; Tamara B Harris; Sami Heikkinen; Raphaël Heinzer; James E Hixson; Georg Homuth; M Arfan Ikram; Pirjo Komulainen; Jose E Krieger; Jiwon Lee; Jingmin Liu; Kurt K Lohman; Annemarie I Luik; Reedik Mägi; Lisa W Martin; Thomas Meitinger; Andres Metspalu; Yuri Milaneschi; Mike A Nalls; Jeff O'Connell; Annette Peters; Patricia Peyser; Olli T Raitakari; Alex P Reiner; Patrick C N Rensen; Treva K Rice; Stephen S Rich; Till Roenneberg; Jerome I Rotter; Pamela J Schreiner; James Shikany; Stephen S Sidney; Mario Sims; Colleen M Sitlani; Tamar Sofer; Konstantin Strauch; Morris A Swertz; Kent D Taylor; André G Uitterlinden; Cornelia M van Duijn; Henry Völzke; Melanie Waldenberger; Robert B Wallance; Ko Willems van Dijk; Caizheng Yu; Alan B Zonderman; Diane M Becker; Paul Elliott; Tõnu Esko; Christian Gieger; Hans J Grabe; Timo A Lakka; Terho Lehtimäki; Kari E North; Brenda W J H Penninx; Peter Vollenweider; Lynne E Wagenknecht; Tangchun Wu; Yong-Bing Xiang; Wei Zheng; Donna K Arnett; Claude Bouchard; Michele K Evans; Vilmundur Gudnason; Sharon Kardia; Tanika N Kelly; Stephen B Kritchevsky; Ruth J F Loos; Alexandre C Pereira; Mike Province; Bruce M Psaty; Charles Rotimi; Xiaofeng Zhu; Najaf Amin; L Adrienne Cupples; Myriam Fornage; Ervin F Fox; Xiuqing Guo; W James Gauderman; Kenneth Rice; Charles Kooperberg; Patricia B Munroe; Ching-Ti Liu; Alanna C Morrison; Dabeeru C Rao; Diana van Heemst; Susan Redline
Journal:  Nat Commun       Date:  2019-11-12       Impact factor: 14.919

7.  GxEsum: a novel approach to estimate the phenotypic variance explained by genome-wide GxE interaction based on GWAS summary statistics for biobank-scale data.

Authors:  Jisu Shin; Sang Hong Lee
Journal:  Genome Biol       Date:  2021-06-21       Impact factor: 13.583
  7 in total

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