Epistasis refers to changes in the effect on phenotype of a unit of genetic information, such as a single nucleotide polymorphism or a gene, dependent on the context of other genetic units. Such interactions are both biologically plausible and good candidates to explain observations which are not fully explained by an additive heritability model. However, the search for epistasis has so far largely failed to recover this missing heritability. We identify key challenges and propose that future works need to leverage idealized systems, known biology and even previously identified epistatic interactions, in order to guide the search for new interactions.
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http://dx.doi.org/10.1186/s13059-024-03427-z | DOI Listing |
medRxiv
November 2024
Centre de Recherche du CHUM, and Faculty of Medicine, University of Montreal, QC, Canada.
Initially introduced in 1909 by William Bateson, classic epistasis (genetic variant interaction) refers to the phenomenon that one variant prevents another variant from a different locus from manifesting its effects. The potential effects of genetic variant interactions on complex diseases have been recognized for the past decades. Moreover, It has been studied and demonstrated that leveraging the combined SNP effects within the genetic block can significantly increase calculation power, reducing background noise, ultimately leading to novel epistasis discovery that the single SNP statistical epistasis study might overlook.
View Article and Find Full Text PDFGenome Biol
November 2024
Commonwealth Scientific and Industrial Research Organisation, Westmead, Australia.
Epistasis refers to changes in the effect on phenotype of a unit of genetic information, such as a single nucleotide polymorphism or a gene, dependent on the context of other genetic units. Such interactions are both biologically plausible and good candidates to explain observations which are not fully explained by an additive heritability model. However, the search for epistasis has so far largely failed to recover this missing heritability.
View Article and Find Full Text PDFCell Mol Neurobiol
November 2024
Division of Addiction Research and Education, Center for Sports, Exercise, and Mental Health, Western University Health Sciences, Pomona, CA, USA.
The global public health addiction crisis has been stark, with over 932,400 deaths in the USA and Canada from opioid overdose since 1999-2020, surpassing the mortality rates at the top of the HIV/AIDS epidemic. Both nations exhibit opioid consumption rates significantly above the norm for developed countries. Analgesic type of opioids present both therapeutic benefits and substantial health risks, necessitating balanced drug regulation, careful prescribing, and dedicated opioid stewardship.
View Article and Find Full Text PDFPLoS One
October 2024
College of Computer Science and Technology, Changchun University, Changchun City, Jilin Province, China.
Genome-wide association studies typically considers epistatic interactions as a crucial factor in exploring complex diseases. However, the current methods primarily concentrate on the detection of two-order epistatic interactions, with flaws in accuracy. In this work, we introduce a novel method called Epi-SSA, which can be better utilized to detect high-order epistatic interactions.
View Article and Find Full Text PDFNucleic Acids Res
September 2024
Data Science in Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany.
Most heritable diseases are polygenic. To comprehend the underlying genetic architecture, it is crucial to discover the clinically relevant epistatic interactions (EIs) between genomic single nucleotide polymorphisms (SNPs) (1-3). Existing statistical computational methods for EI detection are mostly limited to pairs of SNPs due to the combinatorial explosion of higher-order EIs.
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