Keller-Evans Rachel B, Munafo Daniela, Ross Tristen, Rudawsky Sarah, Savol Andrej, Huang Richard S P
Foundation Medicine, Inc., Cambridge, MA, United States.
Oncologist. 2024 Dec 6;29(12):e1786-e1789. doi: 10.1093/oncolo/oyae226.
While there is great potential for unbiased next-generation sequencing (NGS) approaches-eg, whole transcriptome sequencing (WTS)-for exploration, discovery, and clinical application in the realm of oncology, there are limitations that should be considered when relying on these methodologies for clinical decision making. When using WTS for the detection of clinically relevant gene fusions in tumor specimens, a key consideration is whether a limited coverage depth (approximately 30-50X) is sufficient for detecting these events, especially in samples with low tumor purity. We demonstrate the reduced sensitivity of both a commercial WTS assay for the detection of clinically relevant fusions in analytical validation control samples and of a research use only (RUO) WTS assay for the detection of clinically relevant fusions in real-world clinical samples compared to RNA comprehensive genomic profiling (CGP). Notably, the RUO WTS assay would not have reported 30% (6/20) of fusions detected using RNA CGP assays in fusion-positive tumor samples, highlighting a potential disadvantage of broader sequencing.
虽然在肿瘤学领域，无偏倚的下一代测序（NGS）方法（例如全转录组测序（WTS））在探索、发现和临床应用方面具有巨大潜力，但在依靠这些方法进行临床决策时，仍有一些局限性需要考虑。当使用WTS检测肿瘤标本中临床相关的基因融合时，一个关键的考虑因素是有限的覆盖深度（约30 - 50X）是否足以检测到这些事件，尤其是在肿瘤纯度较低的样本中。与RNA综合基因组分析（CGP）相比，我们证明了用于分析验证对照样本中临床相关融合检测的商业WTS检测方法以及仅用于研究（RUO）的WTS检测方法在检测真实世界临床样本中临床相关融合时的敏感性降低。值得注意的是，在融合阳性肿瘤样本中，RUO WTS检测方法不会报告使用RNA CGP检测方法检测到的30%（6/20）的融合，这凸显了更广泛测序的一个潜在缺点。
