文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期,新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

蛋白质稳定性与AlphaMissense评分的整合改善了对p53错义及框内氨基酸缺失变体的生物信息学影响预测。

Integration of protein stability and AlphaMissense scores improves bioinformatic impact prediction for p53 missense and in-frame amino acid deletion variants.

作者信息

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

机构信息

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.

出版信息

Am J Hum Genet. 2025 May 1;112(5):1003-1014. doi: 10.1016/j.ajhg.2025.01.012. Epub 2025 Apr 14.


DOI:10.1016/j.ajhg.2025.01.012
PMID:40233742
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12120181/
Abstract

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.

摘要

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。

相似文献

[1]
Integration of protein stability and AlphaMissense scores improves bioinformatic impact prediction for p53 missense and in-frame amino acid deletion variants.

Am J Hum Genet. 2025-5-1

[2]
ACMG/AMP interpretation of BRCA1 missense variants: Structure-informed scores add evidence strength granularity to the PP3/BP4 computational evidence.

Am J Hum Genet. 2025-5-1

[3]
Improved, ACMG-compliant, in silico prediction of pathogenicity for missense substitutions encoded by TP53 variants.

Hum Mutat. 2018-6-5

[4]
A quantitative model to predict pathogenicity of missense variants in the TP53 gene.

Hum Mutat. 2019-3-18

[5]
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

Nucleic Acids Res. 2006-3-6

[6]
Evaluating novel in silico tools for accurate pathogenicity classification in epilepsy-associated genetic missense variants.

Epilepsia. 2024-12

[7]
The performance of AlphaMissense to identify genes influencing disease.

HGG Adv. 2024-10-10

[8]
Using AI-predicted protein structures as a reference to predict loss-of-function activity in tumor suppressor breast cancer genes.

Comput Struct Biotechnol J. 2024-10-5

[9]
Making sense of missense: challenges and opportunities in variant pathogenicity prediction.

Dis Model Mech. 2024-12-1

[10]
Comprehensive evaluation of AlphaMissense predictions by evidence quantification for variants of uncertain significance.

Front Genet. 2024-12-10

引用本文的文献

[1]
Structural biology in variant interpretation: Perspectives and practices from two studies.

Am J Hum Genet. 2025-5-1

本文引用的文献

[1]
Calibration of additional computational tools expands ClinGen recommendation options for variant classification with PP3/BP4 criteria.

Genet Med. 2025-3-10

[2]
Accurate structure prediction of biomolecular interactions with AlphaFold 3.

Nature. 2024-6

[3]
Accurate proteome-wide missense variant effect prediction with AlphaMissense.

Science. 2023-9-22

[4]
Computational modeling and prediction of deletion mutants.

Structure. 2023-6-1

[5]
Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2.

Br J Cancer. 2023-6

[6]
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.

Nucleic Acids Res. 2022-1-7

[7]
Highly accurate protein structure prediction with AlphaFold.

Nature. 2021-8

[8]
Specifications of the ACMG/AMP variant interpretation guidelines for germline TP53 variants.

Hum Mutat. 2021-3

[9]
Analyzing Protein Disorder with IUPred2A.

Curr Protoc Bioinformatics. 2020-6

[10]
Biophysical and Mechanistic Models for Disease-Causing Protein Variants.

Trends Biochem Sci. 2019-1-31

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索