为了简化变体分类:ClinVar病原变体的变体命名法和语法在注释工具中存在差异
Yu-An Chen1,2, Tzu-Hang Yuan3,4, Jia-Hsin Huang4
1Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, 10617, Taiwan.
像ANNOVAR,SnpEff和VEP这样的工具之间的注释差异挑战了遗传变体的解释. 标准化成绩单和交叉验证结果对于准确的临床报告至关重要.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 临床遗传学 临床遗传学
背景情况:
- 高通量测序推进了遗传疾病的诊断.
- 解释变异性致病性仍然是一个重大挑战.
- 人类基因组变异协会 (HGVS) 标注中的差异阻碍了进展.
研究的目的:
- 评估ANNOVAR,SnpEff和VEP之间的注释对应性.
- 评估HGVS命名体系,编码影响和ACMG标准的一致性.
- 确定变异性致病性解释中的挑战.
主要方法:
- 分析了164549种ClinVar变种.
- 使用的HGVS命名结构字符串匹配比较.
- 评估编码影响和推断的ACMG标准.
主要成果:
- 观察到的可变一致率为:HGVSc的58.52%,HGVSp的84.04%,编码影响的85.58%.
- 在HGVSc比赛中SnpEff领先 (0.988),在HGVSp比赛中VEP领先 (0.977).
- 功能丧失 (LoF) 和PVS1解释中的显著差异影响了病原性,冒着错误阴性结果的风险.
结论:
- 标注差异对变异性致病性解释提出了关键挑战.
- 标准化转录集对于可靠的遗传变体解释至关重要.
- 在临床实践中,对各种注释工具进行系统的交叉验证至关重要.
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