PDF(Pubmed)
Abstract：
The identification of gene fusions has become an integral part of soft tissue and bone tumour diagnosis. We investigated the added value of targeted RNA-based sequencing (targeted RNA-seq, Archer FusionPlex) to our current molecular diagnostic workflow of these tumours, which is based on fluorescence in situ hybridisation (FISH) for the detection of gene fusions using 25 probes. In a series of 131 diagnostic samples targeted RNA-seq identified a gene fusion, BCOR internal tandem duplication or ALK deletion in 47 cases (35.9%). For 74 cases, encompassing 137 FISH analyses, concordance between FISH and targeted RNA-seq was evaluated. A positive or negative FISH result was confirmed by targeted RNA-seq in 27 out of 49 (55.1%) and 81 out of 88 (92.0%) analyses, respectively. While negative concordance was high, targeted RNA-seq identified a canonical gene fusion in seven cases despite a negative FISH result. The 22 discordant FISH-positive analyses showed a lower percentage of rearrangement-positive nuclei (range 15-41%) compared to the concordant FISH-positive analyses (>41% of nuclei in 88.9% of cases). Six FISH analyses (in four cases) were finally considered false positive based on histological and targeted RNA-seq findings. For the EWSR1 FISH probe, we observed a gene-dependent disparity (p = 0.0020), with 8 out of 35 cases showing a discordance between FISH and targeted RNA-seq (22.9%). This study demonstrates an added value of targeted RNA-seq to our current diagnostic workflow of soft tissue and bone tumours in 19 out of 131 cases (14.5%), which we categorised as altered diagnosis (3 cases), added precision (6 cases), or augmented spectrum (10 cases). In the latter subgroup, four novel fusion transcripts were found for which the clinical relevance remains unclear: NAB2::NCOA2, YAP1::NUTM2B, HSPA8::BRAF, and PDE2A::PLAG1. Overall, targeted RNA-seq has proven extremely valuable in the diagnostic workflow of soft tissue and bone tumours.
摘要：
基因融合的鉴定已成为软组织和骨肿瘤诊断不可或缺的一部分。我们调查了基于靶向RNA的测序的附加值(靶向RNA-seq，ArcherFusionPlex）对我们当前这些肿瘤的分子诊断工作流程，它基于荧光原位杂交（FISH），用于使用25种探针检测基因融合。在一系列131个诊断样本中，靶向RNA-seq鉴定了一个基因融合体，BCOR内部串联复制或ALK缺失47例(35.9%)。对于74个案例，包括137个FISH分析，评估了FISH和靶向RNA-seq之间的一致性。在49个分析中的27个（55.1％）和88个分析中的81个（92.0％）中，通过靶向RNA-seq证实了FISH结果为阳性或阴性。分别。虽然负一致性很高，尽管FISH结果为阴性，但靶向RNA-seq在7例中鉴定出了规范的基因融合。22个不一致的FISH阳性分析显示，与一致的FISH阳性分析（88.9％的病例中>41％的细胞核）相比，重排阳性细胞核的百分比较低（范围为15-41％）。基于组织学和靶向RNA-seq发现,六个FISH分析(在四个病例中)最终被认为是假阳性。对于EWSR1FISH探头,我们观察到基因依赖性差异(p=0.0020)，35例中有8例显示FISH和靶向RNA-seq之间的不一致（22.9%）。这项研究表明，在131例中的19例（14.5％）中，靶向RNA-seq对我们当前的软组织和骨肿瘤诊断工作流程具有附加价值。我们归类为改变诊断（3例），增加精度(6例)，或扩大频谱（10例）。在后一个亚组中，发现了四个新的融合转录本，其临床相关性尚不清楚：NAB2::NCOA2，YAP1::NUTM2B，HSPA8::BRAF,和PDE2A::PLAG1。总的来说,靶向RNA-seq已被证明在软组织和骨肿瘤的诊断工作流程中非常有价值。
