MutAnt:突变注释工具预测了误解突变的有害性,并改进了转录组学中的突变调用
Aleksandr Sarachakov1,2, Anastasiya Yudina1, Viktor Svekolkin1
1BostonGene Corporation, 95 Sawyer Road, Waltham, MA, 02453, USA.
Human genetics
|December 2, 2025
概括
机器学习工具MutAnt准确地区分了引起疾病的突变与中性遗传变异. 这有助于通过改善变异分类和体质突变检测来改善临床基因组学.
科学领域:
- 基因组学和生物信息学
- 计算生物学 计算生物学
- 临床基因组学 临床基因组学
背景情况:
- 致病变体可以通过功能丧失,功能增加或其他机制引起孟德尔病或癌症.
- 解释罕见和新型变异具有挑战性,需要计算工具来区分有害突变和中性变异.
- 准确的变种分类对于临床基因组学和了解疾病机制至关重要.
研究的目的:
- 开发和评估基于机器学习的突变元注释器MutAnt.
- 评估MutAnt使用多种变体特性区分有害变体和中性变体的能力.
- 探索MutAnt在改善体质变异调用方面的实用性及其与功能测试的相关性.
主要方法:
- 开发 MutAnt,一种在大型,临床相关的变体数据集上训练的机器学习模型.
- 将多个变体属性和来自其他算法的同步预测纳入 MutAnt 的训练中.
- 使用F1和ROC-AUC得分,与功能测试 (深度突变扫描) 的相关性以及蛋白质稳定性测量来评估MutAnt的性能.
主要成果:
- 在保留数据集上,MutAnt获得了高F1和ROC-AUC得分 (0.88-0.99).
- MutAnt的有害性预测与BRCA1,PTEN和p53的功能评分 (ρ = 0.28-0.61) 和蛋白质稳定性相关.
- 与标准方法相比,MutAnt改善了从RNA测序数据中调用的体质变异.
结论:
- MutAnt在区分中性和破坏蛋白质的突变方面表现出很高的性能.
- 该工具提供了精确校准的概率得分,与实验功能数据相关联.
- MutAnt在变体分类和基因组分析中显示出显著的临床实用性潜力.
相关概念视频
Nonsense-mediated mRNA Decay
11.6K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
11.6K
Mutations
94.3K
Overview
94.3K
Mutations
42.6K
Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
42.6K
Point and Frameshift Mutations
780
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
780
Mismatch Repair
6.2K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
6.2K


