Guidelines for releasing a variant effect predictor

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  • dc.contributor.author Livesey, Benjamin J.
  • dc.contributor.author Badonyi, Mihaly
  • dc.contributor.author Dias, Mafalda
  • dc.contributor.author Frazer, Jonathan
  • dc.contributor.author Kumar, Sushant
  • dc.contributor.author Lindorff-Larsen, Kresten
  • dc.contributor.author McCandlish, David M.
  • dc.contributor.author Orenbuch, Rose
  • dc.contributor.author Shearer, Courtney A.
  • dc.contributor.author Muffley, Lara
  • dc.contributor.author Foreman, Julia
  • dc.contributor.author Glazer, Andrew M.
  • dc.contributor.author Lehner, Ben, 1978-
  • dc.contributor.author Marks, Debora S.
  • dc.contributor.author Roth, Frederick P.
  • dc.contributor.author Rubin, Alan F.
  • dc.contributor.author Starita, Lea M.
  • dc.contributor.author Marsh, Joseph A.
  • dc.date.accessioned 2025-09-02T06:32:35Z
  • dc.date.available 2025-09-02T06:32:35Z
  • dc.date.issued 2025
  • dc.description.abstract Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein engineering. Many different VEPs have been released, and there is tremendous variability in their underlying algorithms, outputs, and the ways in which the methodologies and predictions are shared. This leads to considerable difficulties for users trying to navigate the selection and application of VEPs. Here, to address these issues, we provide guidelines and recommendations for the release of novel VEPs.
  • dc.description.sponsorship MD and J Frazer are supported by the Spanish Ministry of Science and Innovation (PID2022-140793NA-I00). KLL received funding from the Novo Nordisk Foundation (NNF18OC0033950). DMM received funding from the National Institutes of Health (NIH) (R35GM133613). RO and DSM are supported by the Chan Zuckerberg Initiative Neurodegeneration Challenge Network (CZI2018-191853). LM, LMS, and FPR received funding from the NIH (RM1HG010461), and FPR also received funding from NIH grant UM1HG011989. J Foreman received funding from the Wellcome Trust (WT223718/Z/21/Z). AMG received funding from the NIH (R35GM150465). BL received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 883742). DSM received funding from the NIH (1R01CA260415). AFR received funding from the NIH (UM1HG011969, RM1HG010461, R01HG013025) and grant funding from the Australian Government. JAM is supported by the ERC (grant agreement No. 101001169) and by the Medical Research Council (MRC) Human Genetics Unit core grant (MC_UU_00035/9).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, et al. Guidelines for releasing a variant effect predictor. Genome Biol. 2025 Apr 15;26(1):97. DOI: 10.1186/s13059-025-03572-z
  • dc.identifier.doi http://dx.doi.org/10.1186/s13059-025-03572-z
  • dc.identifier.issn 1474-7596
  • dc.identifier.uri http://hdl.handle.net/10230/71095
  • dc.language.iso eng
  • dc.publisher BioMed Central
  • dc.relation.ispartof Genome Biol. 2025 Apr 15;26(1):97
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2022-140793NA-I00
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/883742
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/101001169
  • dc.rights © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.other Biologia computacional
  • dc.title Guidelines for releasing a variant effect predictor
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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