Goytain Angela, Chang Kenneth Tou En, Goh Jian Yuan, Nielsen Torsten O, Ng Tony L
Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada.
KK Women's and Children's Hospital, Singapore, Singapore; Duke-NUS Medical School, Singapore, Singapore.
J Mol Diagn. 2023 Feb;25(2):121-131. doi: 10.1016/j.jmoldx.2022.11.004. Epub 2022 Dec 9.
Sarcomas are a diverse group of tumors, with >70 subtypes in the current World Health Organization classification, each with distinct biological behavior requiring specific clinical management. A significant portion of sarcomas are molecularly defined by expression of a driver fusion gene; identification of such fusions is the basis of molecular diagnostics in sarcomas, which is of increasing complexity due to the ongoing discovery of new gene fusions. Recently, a multiplex NanoString platform-based assay was developed and clinically implemented, with fusion junction-spanning probes that detect the majority of sarcoma fusion types, with high sensitivity and specificity, and with lower cost and shorter turnaround time than those of targeted next-generation sequencing-based alternatives. Despite the effectiveness of this assay, there are several entities for which fusion-junction probes are not suitable due to multiple possible gene partners or excessive variability at the exon junctions. Here, the development and evaluation of a companion assay are described that uses NanoString-based gene expression analysis to detect aberrant 3'/5' exon expression imbalance and/or total gene overexpression as a surrogate marker for fusion gene rearrangement. This assay evaluates exon imbalance in 23 genes involved in over 25 mesenchymal tumor types and five genes specific to sarcomas with CIC rearrangements. Based on evaluation of 115 retrospectively and 91 prospectively collected cases, an assay sensitivity of 92.8% and specificity of 93.5% are demonstrated.
肉瘤是一组多样化的肿瘤，在当前世界卫生组织的分类中有70多种亚型，每种亚型都有独特的生物学行为，需要特定的临床管理。很大一部分肉瘤在分子水平上由驱动融合基因的表达来定义；识别此类融合是肉瘤分子诊断的基础，由于新基因融合的不断发现，其复杂性日益增加。最近，一种基于NanoString多重平台的检测方法被开发并应用于临床，该方法使用跨越融合接头的探针来检测大多数肉瘤融合类型，具有高灵敏度和特异性，且与基于靶向二代测序的替代方法相比，成本更低、周转时间更短。尽管该检测方法有效，但由于存在多种可能的基因伙伴或外显子接头处的过度变异，仍有几种实体瘤类型不适合使用融合接头探针。在此，描述了一种配套检测方法的开发和评估，该方法使用基于NanoString的基因表达分析来检测异常的3'/5'外显子表达失衡和/或总基因过表达，作为融合基因重排的替代标志物。该检测方法评估了涉及超过25种间叶性肿瘤类型的23个基因以及具有CIC重排的肉瘤特有的5个基因的外显子失衡情况。基于对115例回顾性收集病例和91例前瞻性收集病例的评估，该检测方法的灵敏度为92.8%，特异性为93.5%。
