Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Immuneering Corporation, One Broadway, 14th Floor, Cambridge, MA, 02142, USA.
Sci Data. 2022 Jun 9;9(1):288. doi: 10.1038/s41597-022-01359-6.
The lack of suitable reference genomic material to enable a transparent cross-lab study of oncopanels inspired the SEQC2 Oncopanel Sequencing Working Group to develop four reference samples, sequenced with eight oncopanels at independent test laboratories with ultra-deep sequencing depth. This rich, publicly available dataset enabled performance assessment of the clinical applicability of oncopanels. In addition, this dataset present sample opportunities for developing specific and robust bioinformatics pipelines and fine-tuning parameters for more accurate variant calling, investigating ideal sequencing depth for variant calling of a given minimum VAF and variant type, and also recommending best use cases for Unique Molecular Identifier (UMI) technology.
缺乏合适的参考基因组材料，使得对肿瘤panel 进行透明的跨实验室研究变得困难，这促使 SEQC2 肿瘤panel 测序工作组开发了四个参考样本，这些样本在具有超高测序深度的独立测试实验室中使用八个肿瘤panel 进行了测序。这个丰富的、公开可用的数据集使我们能够评估肿瘤panel 的临床适用性。此外，该数据集还为开发特定的和稳健的生物信息学管道提供了样本机会，以便更准确地调用变异，研究给定最小 VAF 和变异类型的变异调用所需的理想测序深度，还推荐了用于独特分子标识符 (UMI) 技术的最佳用例。
