Considerations in the Search for Epistasis

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UDC.coleccionInvestigación
UDC.departamentoEnxeñaría de Computadores
UDC.grupoInvGrupo de Arquitectura de Computadores (GAC)
UDC.institutoCentroCITIC - Centro de Investigación de Tecnoloxías da Información e da Comunicación
UDC.issue296
UDC.journalTitleGenome Biology
UDC.volume25
dc.contributor.authorBalvert, Marleen
dc.contributor.authorCooper-Knock, Johnathan
dc.contributor.authorStamp, Julian
dc.contributor.authorByrne, Ross P.
dc.contributor.authorMourragui, Soufiane
dc.contributor.authorvan Gils, Juami
dc.contributor.authorBenonisdottir, Stefania
dc.contributor.authorSchlüter, Johannes
dc.contributor.authorKenna, Kevin
dc.contributor.authorGonzález-Domínguez, Jorge
dc.date.accessioned2026-07-23T11:58:40Z
dc.date.available2026-07-23T11:58:40Z
dc.date.issued2024
dc.descriptionThe code for the simulated data is available at Github and Zenodo under an MIT license. - Balvert M, Cooper-Knock J, Stamp J, Byrne RP, Mourragui S, van Gils J et al. Population structure confounds regression-based epistasis detection. 2024. Github https://github.com/jdstamp/leiden_paper. - Balvert M, Cooper-Knock J, Stamp J, Byrne RP, Mourragui S, van Gils J, et al. Population structure confounds regression-based epistasis detection. 2024. Zenodo. https://doi.org/10.5281/zenodo.13940750. A Correction to this paper has been published: https://doi.org/10.1186/s13059-025-03477-x (20 January 2025)
dc.description.abstract[Abstract]: 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.
dc.description.sponsorshipWe also thank the Artificial Intelligence Journal, the Company of Biologists, the Netherlands Organization for Scientific Research (Veni grant VI.Veni.192.043), Bielefeld University, Ronin, and funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreements No 956229 (ALPACA) and No 872539 (PANGAIA) for providing funding for the workshop. R.P.B. is supported by funding from the Motor Neurone Disease Association (Byrne/Oct22/979–799). J.C.K. was supported by the Wellcome Trust (216596/Z/19/Z). C.H./J.C.K. are supported by the MNDA (899–792). M.B. is supported by the Netherlands Organization for Scientific Research (Veni grant VI.Veni.192.043). M.P.S. is supported by the National Institutes of Health (CEGS 5P50HG00773504, 1P50HL083800, 1R01HL101388, 1R01-HL122939, S10OD025212, P30DK116074, and UM1HG009442).
dc.description.sponsorshipNetherlands. Nederlandse Organisatie voor Wetenschappelijk Onderzoek; VI.Veni.192.043
dc.description.sponsorshipUnited Kingdom. Motor Neurone Disease Association; Byrne/Oct22/979–799
dc.description.sponsorshipUnited Kingdom. Motor Neurone Disease Association; 899–792
dc.description.sponsorshipWellcome Trust; 216596/Z/19/Z
dc.description.sponsorshipUnited States. National Institutes of Health; 5P50HG00773504
dc.description.sponsorshipUnited States. National Institutes of Health; 1P50HL083800
dc.description.sponsorshipUnited States. National Institutes of Health; 1R01HL101388
dc.description.sponsorshipUnited States. National Institutes of Health; 1R01-HL122939
dc.description.sponsorshipUnited States. National Institutes of Health; S10OD025212
dc.description.sponsorshipUnited States. National Institutes of Health; P30DK116074
dc.description.sponsorshipUnited States. National Institutes of Health; UM1HG009442
dc.description.urihttps://doi.org/10.1186/s13059-025-03477-x
dc.identifier.citationBalvert, M., Cooper-Knock, J., Stamp, J. et al. Considerations in the search for epistasis. Genome Biol 25, 296 (2024). https://doi.org/10.1186/s13059-024-03427-z
dc.identifier.doi10.1186/s13059-024-03427-z
dc.identifier.issn1474-760X
dc.identifier.urihttps://hdl.handle.net/2183/48927
dc.language.isoeng
dc.publisherSpringer Nature
dc.relation.isbasedonhttps://github.com/jdstamp/leiden_paper
dc.relation.isbasedonhttps://doi.org/10.5281/zenodo.13940750
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/H2020/956229
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/H2020/872539
dc.relation.urihttps://doi.org/10.1186/s13059-024-03427-z
dc.rightsAttribution 4.0 Internationalen
dc.rights.accessRightsopen access
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectEpistasis
dc.subjectGenetic Interaction
dc.subjectGenetics Research
dc.subjectGenetic Linkage
dc.subjectGenetics and Genomics
dc.subjectGenetics Epistatic Interactions in Fitness Landscapes
dc.titleConsiderations in the Search for Epistasis
dc.typejournal article
dc.type.hasVersionVoR
dspace.entity.typePublication
relation.isAuthorOfPublication84d13059-7f4b-4cb5-ac65-0e07a77271f0
relation.isAuthorOfPublication.latestForDiscovery84d13059-7f4b-4cb5-ac65-0e07a77271f0

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