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Detection and replication of epistasis influencing transcription in humans

Gibran Hemani, Konstantin Shakhbazov, Harm-Jan Westra, Tonu Esko, Anjali K. Henders, Allan F. McRae, Jian Yang, Greg Gibson, Nicholas G. Martin, Andres Metspalu, Lude Franke, Grant W. Montgomery (+2 others)
2014 Nature  
The extent to which epistasis influences complex traits 1 and contributes to their variation 2,3 is a fundamental question in evolution and human genetics.  ...  in human traits 7, 8 .  ...  Acknowledgments We are grateful to the volunteers for their generous participation in these studies. We thank Bill Hill, Chris Haley and Lars Ronnegard for helpful discussions and comments.  ... 
doi:10.1038/nature13005 pmid:24572353 pmcid:PMC3984375 fatcat:eyw2j6n23zbeblqjn4vgiud4vu

Multivariate analysis of regulatory SNPs: empowering personal genomics by considering cis-epistasis and heterogeneity

Stephen D Turner, William S Bush
2011 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
By using cis-epistasis models that account for more variance in gene expression, investigators may improve the power and replicability of their genomics studies, and more accurately estimate an individual's  ...  We characterize the structural and statistical nature of these 79 cis-epistasis models, and show that interacting regulatory SNPs often lie far apart from each other and can be quite distant from the gene  ...  From these points, we hypothesize that combinations of SNPs within the 500 kb window of potential transcriptional influence will alter gene expression in humans in a non-linear fashion, here dubbed cis-epistasis  ... 
pmid:21121055 pmcid:PMC3159159 fatcat:peucxw4ma5hhjmqetcsejcqm74

MULTIVARIATE ANALYSIS OF REGULATORY SNPS: EMPOWERING PERSONAL GENOMICS BY CONSIDERING CIS-EPISTASIS AND HETEROGENEITY [chapter]

STEPHEN D. TURNER, WILLIAM S. BUSH
2010 Biocomputing 2011  
By using cis-epistasis models that account for more variance in gene expression, investigators may improve the power and replicability of their genomics studies, and more accurately estimate an individual's  ...  We characterize the structural and statistical nature of these 79 cis-epistasis models, and show that interacting regulatory SNPs often lie far apart from each other and can be quite distant from the gene  ...  From these points, we hypothesize that combinations of SNPs within the 500 kb window of potential transcriptional influence will alter gene expression in humans in a non-linear fashion, here dubbed cis-epistasis  ... 
doi:10.1142/9789814335058_0029 fatcat:dus3qeohavfrxdozph3xp6v24e

Are Interactions between cis -Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts?

Alexandra E. Fish, John A. Capra, William S. Bush
2016 American Journal of Human Genetics  
The importance of epistasis-or statistical interactions between genetic variants-to the development of complex disease in humans has been controversial.  ...  Many of these interactions replicated in an independent dataset (90 of 803 tested, Bonferroni threshold).  ...  Michael Sivley for their help and advice on this project. This work was supported by a human genetics training grant, T32GM080178, from the NIH.  ... 
doi:10.1016/j.ajhg.2016.07.022 pmid:27640306 pmcid:PMC5065654 fatcat:c73przelzrf2rb3xdaprswwd2i

Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action

Ence Yang, Gang Wang, Jizhou Yang, Beiyan Zhou, Yanan Tian, James J. Cai
2016 Human Molecular Genetics  
Specifically, the epistasis model explains a quarter of the identified evQTLs, of which the formation is attributed to the presence of "third-party" eQTLs that influence the level of gene expression in  ...  ., genomic loci associated with gene expression variance, in humans.  ...  Acknowledgements We thank Candice Brinkmeyer-Langford for critically reading and editing this manuscript.  ... 
doi:10.1093/hmg/ddw314 pmid:28171656 pmcid:PMC6078589 fatcat:getxvsyvcfh6rfscuwud6xuunq

Genome-wide association interaction analysis for Alzheimer's disease

Elena S. Gusareva, Minerva M. Carrasquillo, Céline Bellenguez, Elise Cuyvers, Samuel Colon, Neill R. Graff-Radford, Ronald C. Petersen, Dennis W. Dickson, Jestinah M. Mahachie John, Kyrylo Bessonov, Christine Van Broeckhoven, Denise Harold (+6 others)
2014 Neurobiology of Aging  
A replication analysis in the independent AD cohort from Germany (555 patients and 824 controls) confirmed the discovered epistasis signal (p ¼ 0.036).  ...  This signal was also supported by a meta-analysis approach in 5 independent AD cohorts that was applied in the context of epistasis for the first time.  ...  of Health and Medical Research, FRC (fondation pour la recherche sur le cerveau) and Rotary, and the LABEX (laboratory of excellence program investment for the future) DISTALZ grant (Development of Innovative  ... 
doi:10.1016/j.neurobiolaging.2014.05.014 pmid:24958192 pmcid:PMC4370231 fatcat:ok46qutekjeobghrwvq2jori5y

The Ubiquitous Nature of Epistasis in Determining Susceptibility to Common Human Diseases

Jason H. Moore
2003 Human Heredity  
In this paper, we formulate a working hypothesis that epistasis is a ubiquitous component of the genetic architecture of common human diseases and that complex interactions are more important than the  ...  We review each of these points and then review an analytical strategy called multifactor dimensionality reduction for detecting epistasis.  ...  for Genetic Architecture of Complex Diseases) for many stimulating discussions about the detection and characterization of epistasis.  ... 
doi:10.1159/000073735 pmid:14614241 fatcat:n72v3uzyz5ashfr6py3svewmpu

PTGER4 Expression-Modulating Polymorphisms in the 5p13.1 Region Predispose to Crohn's Disease and Affect NF-κB and XBP1 Binding Sites

Jürgen Glas, Julia Seiderer, Darina Czamara, Giulia Pasciuto, Julia Diegelmann, Martin Wetzke, Torsten Olszak, Christiane Wolf, Bertram Müller-Myhsok, Tobias Balschun, Jean-Paul Achkar, M. Ilyas Kamboh (+4 others)
2012 PLoS ONE  
Epistasis detected between 5p13.1 and ATG16L1 for CD susceptibility in the discovery cohort (p = 5.99610 27 for rs7720838 and rs2241880) could not be replicated in both replication cohorts arguing against  ...  Genotype-phenotype, epistasis and transcription factor binding analyses were performed.  ...  However, as shown in Tables S12 and S13, there was no significant epistasis detected between these gene markers, suggesting that the strong epistasis between 5p13.1 and ATG16L1 found in the German CD discovery  ... 
doi:10.1371/journal.pone.0052873 pmid:23300802 pmcid:PMC3531335 fatcat:avbrolendbfvjojpobj2nzkveu

Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action [article]

Ence Yang, Gang Wang, Jizhou Yang, Beiyan Zhou, Yanan Tian, James J Cai
2015 bioRxiv   pre-print
Specifically, the epistasis model explains a quarter of the identified evQTLs, of which the formation is attributed to the presence of "third-party" eQTLs that influence the level of gene expression in  ...  ., genomic loci associated with gene expression variance, in humans.  ...  Acknowledgements We thank Candice Brinkmeyer-Langford for critically reading and editing this manuscript.  ... 
doi:10.1101/026393 fatcat:3zrf6rkybrf2zj5yurzhdd53wq

Genome-wide search for higher order epistasis as modifiers of treatment effects on bone mineral density in childhood cancer survivors

Cindy Im, Kirsten K. Ness, Sue C. Kaste, Wassim Chemaitilly, Wonjong Moon, Yadav Sapkota, Russell J. Brooke, Melissa M. Hudson, Leslie L. Robison, Yutaka Yasui, Carmen L. Wilson
2018 European Journal of Human Genetics  
In anticipation that power to detect higher order epistasis would be low using an exhaustive search and a Bonferroni-corrected threshold for genome-wide significance (e.g., P < 5.6 × 10 −14 ), a novel  ...  Our study demonstrates the utility of a hypothesis-driven approach in revealing epistasis associated with complex traits.  ...  methods to detect higher order epistasis.  ... 
doi:10.1038/s41431-017-0050-x pmid:29348692 fatcat:ksixjgb2ejebbjpisizl6lsfrm

Are Genetic Interactions Influencing Gene Expression Evidence for Biological Epistasis or Statistical Artifacts? [article]

Alexandra Fish, John A. Capra, William S Bush
2015 bioRxiv   pre-print
The importance of epistasis, or statistical interactions between genetic variants, to the development of complex disease in humans has long been controversial.  ...  Every replicated interaction could be explained by at least one of these confounders, and replication in independent datasets did not protect against this issue.  ...  Acknowledgements We thank Laura Wiley for normalizing gene expression values within the replication dataset. We also thank Jacob Hall, Corinne Simonti, and R.  ... 
doi:10.1101/020479 fatcat:cu6sxci3lnbr3akytakr64tvjy

Characterisation of Genome-Wide Association Epistasis Signals for Serum Uric Acid in Human Population Isolates

Wenhua Wei, Gibran Hemani, Andrew A. Hicks, Veronique Vitart, Claudia Cabrera-Cardenas, Pau Navarro, Jennifer Huffman, Caroline Hayward, Sara A. Knott, Igor Rudan, Peter P. Pramstaller, Sarah H. Wild (+7 others)
2011 PLoS ONE  
SNPs and the genome and jointly explaining 8.0% of the phenotypic variance in SUA levels (3.4% by interaction components).  ...  Genome-wide association (GWA) studies have identified a number of loci underlying variation in human serum uric acid (SUA) levels with the SLC2A9 gene having the largest effect identified so far.  ...  We like to thank all of the staff and participants in the MICROS, VIS, KORCULA and SOCCS studies, in particular those who contributed to data and sample collection, genotyping, trait measurement and data  ... 
doi:10.1371/journal.pone.0023836 pmid:21886828 pmcid:PMC3158795 fatcat:s7ke2x7z2vf2da3ztffcg6xjpa

Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis

Jason H. Moore, Scott M. Williams
2005 Bioessays  
First, when does statistical evidence of epistasis in human populations imply underlying biomolecular interactions in the etiology of disease?  ...  Second, when do biomolecular interactions produce patterns of statistical epistasis in human populations?  ...  Thanks are also extended to two anonymous reviewers and Adam Wilkins for their very thoughtful comments, criticisms, and suggestions that were taken to heart in preparing the final version of the manuscript  ... 
doi:10.1002/bies.20236 pmid:15892116 fatcat:dp46buffg5aubjkrb6tnovby3q

Practical aspects of genome-wide association interaction analysis

Elena S. Gusareva, Kristel Van Steen
2014 Human Genetics  
Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK) and our colleagues François Van Lishout  ...  Mahachie John and Kyrylo Bessonov from the Systems and Modeling Unit, Montefiore Institute, University of Liege, Belgium without whom the development of the GWAI protocol would not have been possible.  ...  Note that analytic epistasis detection strategies vary greatly in the way LD patterns influence increased false positives [redundant epistasis due to LD (Moore et al. 2007) ], and that depending on the  ... 
doi:10.1007/s00439-014-1480-y pmid:25164382 fatcat:zue2ifjuhjdm5dk4bp7rhbqi5y

Atlas of epistasis [article]

Clément Chatelain, Samuel Lessard, Vincent Thuillier, Cedric Carliez, Deepak Rajpal, Franck Augé
2021 medRxiv   pre-print
Most of the variants in interactions (82%) were more than 1Mb apart and cis-epistasis was hardly found outside the HLA region.  ...  We identified 152,519 genome wide significant interactions in 68 distinct phenotypes, and 3,398 interactions in 19 phenotypes were successfully replicated in independent cohorts from the Finngen consortium  ...  Authors acknowledge the Finngen consortium for access to data used for replication cohorts.  ... 
doi:10.1101/2021.03.17.21253794 fatcat:3ouiisebhnhxfbe3aqs4oun3mq
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