对潜在拼接变异的常规RNA分析有助于基因组诊断,并揭示了in silico预测工具的局限性
Mark Drost1, Jordy Dekker1, Federico Ferraro1
1Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, PO Box 2040, 3000 Rotterdam, the Netherlands.
HGG advances
|September 24, 2025
概括
患者细胞的常规RNA分析有效地解释了影响mRNA前拼接的遗传变异,重新分类了许多意义不明的变异 (VUS),并提高了遗传疾病的诊断准确性.
科学领域:
- 分子生物学分子生物学
- 遗传学 是一个遗传学.
- 生物信息学是一种生物信息学.
背景情况:
- 影响mRNA前拼接的DNA变异是遗传疾病的重要原因.
- 在没有实验验证的情况下,解释这些拼接改变变异是具有挑战性的.
- 目前的指导方针建议实验性表征,但其常规诊断价值尚不清楚.
研究的目的:
- 评估mRNA前拼接分析在疑似改变拼接变异的诊断环境中的实用性.
- 使用基于RNA的分析来确定不确定的重要变异 (VUS) 的重新分类率.
- 对实验数据进行in silico拼接预测工具的性能进行基准测试.
主要方法:
- 在202名患者的细胞中,使用RT-PCR分析了mRNA前拼接,随后进行凝电泳和桑格序列或外子捕获.
- 不确定意义的变异 (VUS) 根据观察到的拼接效应被重新分类.
- 在经过验证的数据集上评估了拼接预测算法 (SpliceAI,SQUIRLS,SPiP,Pangolin,Alamut) 的性能.
主要成果:
- 在63% (128/202) 的测试变体中检测到拼接效应.
- RNA分析导致重新分类的54% (96/177) 的最初分类的VUS.
- 48% (85/177) 的VUS升级为可能致病性或致病性,显示出显著的诊断影响.
- 在 silico 工具显示了可变的性能,没有单一的工具准确地分类所有变体.
结论:
- 基于RNA的分析提供了一个有价值的框架,用于对变异变异的分子诊断.
- 对患者mRNA拼接的常规测试显著提高了对遗传变异的解释.
- 在状拼接预测工具有局限性,实验验证对于准确的变体分类至关重要.
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