Genome‐wide interaction study reveals epistatic interactions for beef lipid‐related traits in Nellore cattle

2021 ◽  
Author(s):  
S. T. Amorim ◽  
N. B. Stafuzza ◽  
S. Kluska ◽  
E. Peripolli ◽  
A. S. C. Pereira ◽  
...  
Keyword(s):  
Interaction Study ◽  
Epistatic Interactions ◽  
Genome Wide ◽  
Nellore Cattle

EpiPen: An R Package to Investigate Two-Locus Epistatic Models

2014 ◽  
Vol 17 (4) ◽  
Author(s):  
Raymond K. Walters ◽  
Charles Laurin ◽  
Gitta H. Lubke
Keyword(s):  
Power Analysis ◽  
R Package ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Epistatic Interactions ◽  
Model Interpretation ◽  
Genome Wide ◽  
Using Data ◽  
Power Analyses

Epistasis is a growing area of research in genome-wide studies, but the differences between alternative definitions of epistasis remain a source of confusion for many researchers. One problem is that models for epistasis are presented in a number of formats, some of which have difficult-to-interpret parameters. In addition, the relation between the different models is rarely explained. Existing software for testing epistatic interactions between single-nucleotide polymorphisms (SNPs) does not provide the flexibility to compare the available model parameterizations. For that reason we have developed an R package for investigating epistatic and penetrance models, EpiPen, to aid users who wish to easily compare, interpret, and utilize models for two-locus epistatic interactions. EpiPen facilitates research on SNP-SNP interactions by allowing the R user to easily convert between common parametric forms for two-locus interactions, generate data for simulation studies, and perform power analyses for the selected model with a continuous or dichotomous phenotype. The usefulness of the package for model interpretation and power analysis is illustrated using data on rheumatoid arthritis.

scholarly journals Genome-wide interaction study of gene-by-occupational exposures on respiratory symptoms

2019 ◽  
Vol 122 ◽  
pp. 263-269 ◽  
Author(s):  
Xiang Zeng ◽  
Judith M. Vonk ◽  
Diana A. van der Plaat ◽  
Alen Faiz ◽  
Peter D. Paré ◽  
...  
Keyword(s):  
Respiratory Symptoms ◽  
Occupational Exposures ◽  
Interaction Study ◽  
Genome Wide

scholarly journals Genetic variants in LEKR1 and GALNT10 modulate sex-difference in carotid intima-media thickness: A genome-wide interaction study

2015 ◽  
Vol 240 (2) ◽  
pp. 462-467 ◽  
Author(s):  
Chuanhui Dong ◽  
David Della-Morte ◽  
Ashley Beecham ◽  
Liyong Wang ◽  
Digna Cabral ◽  
...  
Keyword(s):  
Sex Difference ◽  
Genetic Variants ◽  
Intima Media Thickness ◽  
Carotid Intima Media Thickness ◽  
Interaction Study ◽  
Media Thickness ◽  
Genome Wide ◽  
A Genome

Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus )

2014 ◽  
Vol 131 (3) ◽  
pp. 210-216 ◽  
Author(s):  
M.H.A. Santana ◽  
Y.T. Utsunomiya ◽  
H.H.R. Neves ◽  
R.C. Gomes ◽  
J.F. Garcia ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Average Daily Gain ◽  
Bos Indicus ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Nellore Cattle ◽  
Daily Gain

scholarly journals Multi-locus interactions and the build-up of reproductive isolation

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190543 ◽  
Author(s):  
I. Satokangas ◽  
S. H. Martin ◽  
H. Helanterä ◽  
J. Saramäki ◽  
J. Kulmuni
Keyword(s):  
Reproductive Isolation ◽  
Empirical Work ◽  
Hybrid Fitness ◽  
Epistatic Interactions ◽  
Genome Scans ◽  
Theoretical Approaches ◽  
Genome Wide ◽  
Experimental Approaches ◽  
Polymorphism Data

All genes interact with other genes, and their additive effects and epistatic interactions affect an organism's phenotype and fitness. Recent theoretical and empirical work has advanced our understanding of the role of multi-locus interactions in speciation. However, relating different models to one another and to empirical observations is challenging. This review focuses on multi-locus interactions that lead to reproductive isolation (RI) through reduced hybrid fitness. We first review theoretical approaches and show how recent work incorporating a mechanistic understanding of multi-locus interactions recapitulates earlier models, but also makes novel predictions concerning the build-up of RI. These include high variance in the build-up rate of RI among taxa, the emergence of strong incompatibilities producing localized barriers to introgression, and an effect of population size on the build-up of RI. We then review recent experimental approaches to detect multi-locus interactions underlying RI using genomic data. We argue that future studies would benefit from overlapping methods like ancestry disequilibrium scans, genome scans of differentiation and analyses of hybrid gene expression. Finally, we highlight a need for further overlap between theoretical and empirical work, and approaches that predict what kind of patterns multi-locus interactions resulting in incompatibilities will leave in genome-wide polymorphism data. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals Variance heterogeneity genome‐wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Waseem Hussain ◽  
Malachy T. Campbell ◽  
Diego Jarquin ◽  
Harkamal Walia ◽  
Gota Morota
Keyword(s):  
Bread Wheat ◽  
Variance Heterogeneity ◽  
Epistatic Interactions ◽  
Genome Wide

scholarly journals Effect of 6p21 region on lung function is modified by smoking: a genome-wide interaction study

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Boram Park ◽  
Jaehoon An ◽  
Wonji Kim ◽  
Hae Yeon Kang ◽  
Sang Baek Koh ◽  
...  
Keyword(s):  
Lung Function ◽  
Interaction Study ◽  
Genome Wide ◽  
A Genome
Sign in / Sign up

Export Citation Format

Share Document