Guidelines for releasing a variant effect predictor

Livesey, Benjamin J, Badonyi, Mihaly, Dias, Mafalda, Frazer, Jonathan, Kumar, Sushant, Lindorff-Larsen, Kresten, McCandlish, David M, Orenbuch, Rose, Shearer, Courtney A, Muffley, Lara, Foreman, Julia, Glazer, Andrew M, Lehner, Ben, Marks, Debora S, Roth, Frederick P, Rubin, Alan F, Starita, Lea M, Marsh, Joseph A (April 2024) Guidelines for releasing a variant effect predictor. ArXiv. ISSN 2331-8422 (Submitted)

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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 to date, and there is tremendous variability in their underlying algorithms and outputs, and in the ways in which the methodologies and predictions are shared. This leads to considerable challenges for end users in knowing which VEPs to use and how to use them. Here, to address these issues, we provide guidelines and recommendations for the release of novel VEPs. Emphasising open-source availability, transparent methodologies, clear variant effect score interpretations, standardised scales, accessible predictions, and rigorous training data disclosure, we aim to improve the usability and interpretability of VEPs, and promote their integration into analysis and evaluation pipelines. We also provide a large, categorised list of currently available VEPs, aiming to facilitate the discovery and encourage the usage of novel methods within the scientific community.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations
CSHL Authors:	McCandlish, David
Communities:	CSHL labs > McCandlish lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	16 April 2024
Date Deposited:	10 May 2024 15:08
Last Modified:	10 May 2024 15:08
PMCID:	PMC11065047
URI:	https://repository.cshl.edu/id/eprint/41544

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