Rotenberg Nitsan, Fortuno Cristina, Varga Matthew J, Chamberlin Adam C, Ramadane-Morchadi Lobna, Feng Bing-Jian, de la Hoya Miguel, Richardson Marcy E, Spurdle Amanda B
Molecular Cancer Epidemiology Laboratory, QIMR Berghofer MRI, Herston, QLD 4006, Australia; University of Queensland, Brisbane, QLD, Australia.
Molecular Cancer Epidemiology Laboratory, QIMR Berghofer MRI, Herston, QLD 4006, Australia.
Am J Hum Genet. 2025 May 1;112(5):1003-1014. doi: 10.1016/j.ajhg.2025.01.012. Epub 2025 Apr 14.
The clinical classification of germline missense variants and single-amino-acid deletions is challenging. The BayesDel and Align-GVGD bioinformatic prediction tools currently used for ClinGen TP53 variant curation expert panel (VCEP) classification do not directly capture changes in protein folding stability, measured using computed destabilization energies (ΔΔG scores). The AlphaMissense tool recently developed by Google DeepMind to predict pathogenicity for all human proteome missense variants is trained in part using AlphaFold2 architecture. Our study investigated whether protein folding stability and/or AlphaMissense scores could improve impact prediction for p53 missense and single-amino-acid deletion variants. ΔΔG scores were calculated for missense variants using FoldX and for single-amino-acid deletions using an AlphaFold2/RosettaRelax protocol. Residue surface exposure was categorized using relative solvent accessibility (RSA) measures. The predictive values of ΔΔG scores, AlphaMissense, BayesDel, and Align-GVGD were examined using Boruta and binary logistic regression based on functionally defined reference sets. The likelihood ratio (LR) toward pathogenicity was estimated and used to refine optimal categories for predicting variant pathogenicity for different RSA values. We showed that current VCEP predictive approaches for missense variants were improved by integrating ΔΔG scores ≥2.5 kcal/mol for partially buried and buried residues, but better performance was achieved using AlphaMissense with ΔΔG and RSA. For deletion variants, ΔΔG scores ≥4.8 Rosetta energy unit (REU) in buried residues outperformed currently used predictive approaches. Future TP53 VCEP specifications for p53 missense impact prediction may consider AlphaMissense, ΔΔG score, and RSA combined for substitution variants and ΔΔG score alone for deletion variants.
种系错义变体和单氨基酸缺失的临床分类具有挑战性。目前用于临床基因组学TP53变体策展专家小组(VCEP)分类的BayesDel和Align-GVGD生物信息学预测工具不能直接捕捉使用计算的去稳定化能量(ΔΔG分数)测量的蛋白质折叠稳定性变化。谷歌深度思维公司最近开发的用于预测所有人类蛋白质组错义变体致病性的AlphaMissense工具部分使用AlphaFold2架构进行训练。我们的研究调查了蛋白质折叠稳定性和/或AlphaMissense分数是否可以改善对p53错义及单氨基酸缺失变体的影响预测。使用FoldX计算错义变体的ΔΔG分数,使用AlphaFold2/RosettaRelax协议计算单氨基酸缺失的ΔΔG分数。使用相对溶剂可及性(RSA)测量对残基表面暴露进行分类。基于功能定义的参考集,使用Boruta和二元逻辑回归检验ΔΔG分数、AlphaMissense、BayesDel和Align-GVGD的预测值。估计向致病性的似然比(LR),并用于为不同RSA值预测变体致病性细化最佳类别。我们表明,通过整合部分埋藏和埋藏残基的ΔΔG分数≥2.5千卡/摩尔,当前针对错义变体的VCEP预测方法得到了改进,但使用结合了ΔΔG和RSA的AlphaMissense性能更佳。对于缺失变体,埋藏残基中ΔΔG分数≥4.8罗塞塔能量单位(REU)优于目前使用的预测方法。未来TP53 VCEP关于p53错义影响预测的规范可能会考虑对替代变体结合使用AlphaMissense、ΔΔG分数和RSA,对缺失变体单独使用ΔΔG分数。
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