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通过使用来自Sequencing Quality Control 2 (SEQC2) 项目的单个细胞系序列数据,通过手动审查扩展设定的基准测试范围

Binsheng Gong¹, Dan Li¹, Yifan Zhang¹

¹Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.

Scientific reports

|March 26, 2024

概括

创建了一个新的,扩展了一组已知的indel变体,以提高indel调用精密医学生物信息学管道的准确性. 这种丰富的数据集有助于评估各种变异异基因频率的管道性能.

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.
癌症研究癌症研究

背景情况:

准确的内部调用对于精准医学至关重要.
现有的基准测试数据集,比如测序质量控制第二阶段 (SEQC2) 项目的数据集,在范围和翻译相关性方面存在局限性.
需要一个更全面和与癌症相关的已知数据集来评估生物信息学管道.

研究的目的:

创建一个丰富的已知indel集,专注于与癌症相关的地区,以加强indel调用管道的基准测试.
为评估精准医学中使用的生物信息学工具提供一个更适合翻译的资源.
扩大已知的indel设置超出了之前的SEQC2项目的局限性.

主要方法:

一个手动审查过程涉及42名审稿人,两名顾问和三名研究人员的评审小组被聘用来识别和验证额外的项目.
重点是将来自癌症相关基因组区域的indels纳入,以增加翻译相关性.
扩展组的特征是变异性等位基因频率 (VAF),内基因长度和基因组位置 (编码和调节区域).

主要成果:

通过精心的手册审查,已知indel集增加了另外516个indels.
扩展组具有广泛的VAF,在参考样本A中87%低于20%,使得在低VAF的情况下进行基准测试.
大多数indel都低于10个基对,位于编码或基因调节区域内.

结论:

丰富的 benchmarking indel 集与参考样本相结合,为全面评估 indel 呼叫管道提供了强大的资源.
从手动审查过程中获得的洞察力可以为改善独立呼叫管道性能提供信息.
这种扩展的数据集对推进精准医学有价值,因为它可以更准确地检测变种.

关键词:

基准测试 (benchmarking) 是一种比较的方法.生物信息学是一种生物信息学.在英德尔 (Indel) 的房间里.精准医学是一门精准的医学.质量控制质量控制

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