拼接VarDB:一个实验验证的人类拼接变体的全面数据库
Patricia J Sullivan1, Julian M W Quinn2, Weilin Wu2
1Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia; UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia.
American journal of human genetics
|September 3, 2024
概括
拼接VarDB是一个新的数据库,它从数千个基因中整合了超过50,000个拼接变体. 该资源有助于解释影响基因拼接的遗传变异,提高诊断准确度.
科学领域:
- 基因组学就是基因组学.
- 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:
- 拼接变体对遗传疾病有很大贡献,但仅仅使用DNA数据就很难预测.
- 目前基于RNA的分析资源密集,验证的拼接变体数据在ClinVar.Var等公共数据库中是分散的和不足的.
- 这种碎片化阻碍了变体解释,并导致冗余的验证工作.
研究的目的:
- 开发SpliceVarDB,这是一个集中在线数据库,用于影响基因拼接的变异.
- 标准化和协调来自不同实验来源的拼接变体验证数据.
- 为了促进拼接变体的解释,并支持改进的in silico预测工具的开发.
主要方法:
- 编译了超过5万种影响8000多个人类基因拼接的变异.
- 系统地评估了500多个已发表的数据来源,以确定变异拼接原性.
- 建立了一个拼接致病度量表来根据证据强度对变异进行分类.
主要成果:
- 将变种分为"改变拼接" (~25%),"不改变拼接" (~25%) 和"低频改变拼接" (~50%) 的类别.
- 确定了SpliceVarDB中55%的拼接改变变体位于正规拼接站点之外,包括深层内部区域.
- 证明了SpliceVarDB对于变体策划和预测模型开发的实用性.
结论:
- 拼接VarDB为拼接变体数据提供了一个全面的,协调的资源,解决了遗传变体解释中的关键差距.
- 该数据库支持诊断工作流程和先进的in silico拼接预测工具.
- 在https://splicevardb.org上公开访问SpliceVarDB,促进合作研究和改进遗传疾病诊断.
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