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系统地评估罕见的正规拼接位变异对使用功能和in silico方法拼接的影响
Rachel Y Oh1, Ali AlMail2, David Cheerie3
1Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada; Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
HGG advances
|April 25, 2024
概括
大约25%的血液基因中罕见的正规拼接位变异 (CSSV) 不会导致功能丧失 (LoF). 对CSSV效应的in silico预测经常与RNA测序数据不一致,建议在应用致病性标准时谨慎使用.
科学领域:
- 遗传学 遗传学 是一个
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- 常规拼接部位变异 (CSSV) 通常被认为会导致功能丧失 (LoF),并被赋予强有力的致病性证据 (PVS1).
- 血液表达基因中未经选择的罕见CSSVs的精确拼接影响和可预测性仍然不清楚.
研究的目的:
- 通过使用RNA测序 (RNA-seq) 来研究血液表达基因中罕见的CSSVs的拼接后果.
- 评估in silico预测工具和当前指南在评估CSSVs的致病性时的准确性.
主要方法:
- 基因组测序在112个个体中发现了168种罕见的CSSV.
- RNA测序 (RNA-seq) 分析了这些CSSV的拼接影响.
- 在 silico 工具 (SpliceAI,MaxEntScan,AutoPVS1) 和 ClinGen 准则被用于预测.
主要成果:
- 25.6%的CSSV没有通过RNA-seq显示LoF的证据,表现出正常的拼接,框架内变化或异子跳转.
- 在 silico 预测显示了与RNA-seq 发现的有限一致性:SpliceAI (65%),MaxEntScan (63%) 和AutoPVS1 (61%).
结论:
- 很大一部分罕见的CSSV不会导致功能丧失.
- 目前的in silico预测方法和PVS1标准的应用可能需要对CSSV进行重新评估,因为它们与功能性RNA-seq数据的频繁不一致.
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