CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Critical Assessment of Genome Interpretation Consortium (February 2024) CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology, 25 (1). p. 53. ISSN 1474-7596

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URL: https://www.ncbi.nlm.nih.gov/pubmed/38389099

DOI: 10.1186/s13059-023-03113-6

Abstract

BACKGROUND: The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. RESULTS: Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. CONCLUSIONS: Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Item Type:	Paper
Subjects:	bioinformatics ?? Computational Biology ?? bioinformatics > genomics and proteomics ?? Humans ?? ?? Mutation, Missense ?? ?? Phenotype ??
CSHL Authors:	McCombie, W. Richard
Communities:	CSHL labs > McCombie lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	22 February 2024
Date Deposited:	04 Apr 2024 16:42
Last Modified:	04 Apr 2024 16:42
PMCID:	PMC10882881
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41485

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