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基于数据的见解为剪接改变变异评估提供信息。

Data-driven insights to inform splice-altering variant assessment.

作者信息

Sullivan Patricia J, Quinn Julian M W, Ajuyah Pamela, Pinese Mark, Davis Ryan L, Cowley Mark J

机构信息

Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia; University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia.

Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.

出版信息

Am J Hum Genet. 2025 Apr 3;112(4):764-778. doi: 10.1016/j.ajhg.2025.02.012. Epub 2025 Mar 7.

Abstract

Disease-causing genetic variants often disrupt mRNA splicing, an intricate process that is incompletely understood. Thus, accurate inference of which genetic variants will affect splicing and what their functional consequences will be is challenging, particularly for variants outside of the essential splice sites. Here, we describe a set of data-driven heuristics that inform the interpretation of human splice-altering variants (SAVs) based on the analysis of annotated exons, experimentally validated SAVs, and the currently understood principles of splicing biology. We defined requisite splicing criteria by examining around 202,000 canonical protein-coding exons and 19,000 experimentally validated splicing branchpoints. This analysis defined the sequence, spacing, and motif strength required for splicing, with 95.9% of the exons examined meeting these criteria. By considering over 12,000 experimentally validated variants from the SpliceVarDB, we defined a set of heuristics that inform the evaluation of putative SAVs. To ensure the applicability of each heuristic, only those supported by at least 10 experimentally validated variants were considered. This allowed us to establish a measure of spliceogenicity: the proportion of variants at a location (or motif site) that affected splicing in a given context. This study makes considerable advances toward bridging the gap between computational predictions and the biological process of splicing, offering an evidence-based approach to identifying SAVs and evaluating their impact. Our splicing heuristics enhance the current framework for genetic variant evaluation with a robust, detailed, and comprehensible analysis by adding valuable context over traditional binary prediction tools.

摘要

致病基因变异常常会破坏mRNA剪接,这是一个尚未被完全理解的复杂过程。因此,准确推断哪些基因变异会影响剪接以及它们的功能后果是什么具有挑战性,特别是对于基本剪接位点之外的变异。在这里,我们描述了一组数据驱动的启发式方法,这些方法基于对注释外显子、实验验证的剪接改变变异(SAV)以及当前理解的剪接生物学原理的分析,为人类剪接改变变异(SAV)的解释提供信息。我们通过检查约202,000个典型蛋白质编码外显子和19,000个实验验证的剪接分支点来定义必需的剪接标准。该分析确定了剪接所需的序列、间距和基序强度,所检查的外显子中有95.9%符合这些标准。通过考虑来自SpliceVarDB的超过12,000个实验验证的变异,我们定义了一组启发式方法,用于评估推定的SAV。为确保每个启发式方法的适用性,仅考虑那些至少有10个实验验证变异支持的方法。这使我们能够建立一种剪接原性的度量:在给定背景下影响剪接的某个位置(或基序位点)的变异比例。这项研究在弥合计算预测与剪接生物学过程之间的差距方面取得了重大进展,提供了一种基于证据的方法来识别SAV并评估其影响。我们的剪接启发式方法通过在传统二元预测工具的基础上增加有价值的背景信息,以强大、详细且可理解的分析增强了当前的基因变异评估框架。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/74e8/12081236/b7e53bdf7062/gr1.jpg

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