Journal Article

Guidelines for releasing a variant effect predictor

Roth, Frederick P., Marsh, Joseph A., Orenbuch, Rose, Livesey, Benjamin J., Rubin, Alan F., Frazer, Jonathan, Dias, Mafalda, Lehner, Ben, Muffley, Lara, Foreman, Julia, Glazer, Andrew M., McCandlish, David M., Lindorff-Larsen, Kresten, Shearer, Courtney A., Marks, Debora S., Starita, Lea M., Kumar, Sushant, Badonyi, Mihaly

2025

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Algorithms / Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Brief Report / Computational Biology - methods / Energy consumption / Evolutionary Biology / Genetic diversity / Genetic Variation / genome / Guidelines as Topic / Human Genetics / Humans / Life Sciences / Methods / Microbial Genetics and Genomics / Mutation / Plant Genetics and Genomics / Protein engineering / Proteins / Reproducibility / Software / Towards an atlas of variant effects