Medical Oncology, Hospital Clínic, Barcelona, Spain;
Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
Clin Chem. 2017 Mar;63(3):751-760. doi: 10.1373/clinchem.2016.265314. Epub 2017 Jan 10.
Anaplastic lymphoma receptor tyrosine kinase (), ROS proto-oncogene 1, receptor tyrosine kinase (), and ret proto-oncogene () fusions are present in 5%-7% of patients with advanced non-small-cell lung cancer (NSCLC); their accurate identification is critical to guide targeted therapies. FISH and immunohistochemistry (IHC) are considered the gold standards to determine gene fusions, but they have limitations. The nCounter platform is a potentially useful genomic tool for multiplexed detection of gene fusions, but has not been validated in the clinical setting.
Formalin-fixed, paraffin embedded (FFPE) samples from 108 patients with advanced NSCLC were analyzed with an nCounter-based assay and the results compared with FISH, IHC, and reverse transcription PCR (RT-PCR). Data on response to fusion kinase inhibitors was retrospectively collected in a subset of 29 patients.
Of 108 FFPE samples, 98 were successfully analyzed by nCounter (91%), which identified 55 fusion-positive cases (32 , 21 , and 2 ). nCounter results were highly concordant with IHC for ALK (98.5%, CI = 91.8-99.7), while 11 discrepancies were found compared with FISH (87.5% concordance, CI = 79.0-92.9). For , nCounter showed similar agreement with IHC and FISH (87.2% and 85.9%), but a substantial number of samples were positive only by 1 or 2 techniques. Of the 25 patients deriving clinical benefit from fusion kinase inhibitors, 24 were positive by nCounter and 22 by FISH.
nCounter compares favorably with IHC and FISH and can be used for identifying patients with advanced NSCLC positive for // fusion genes.
间变性淋巴瘤激酶受体酪氨酸激酶（）、ROS 原癌基因 1、受体酪氨酸激酶（）和 ret 原癌基因（）融合存在于 5%-7%的晚期非小细胞肺癌（NSCLC）患者中；准确识别这些融合对于指导靶向治疗至关重要。荧光原位杂交（FISH）和免疫组织化学（IHC）被认为是确定基因融合的金标准，但它们存在局限性。nCounter 平台是一种用于融合基因多重检测的潜在有用的基因组工具，但尚未在临床环境中得到验证。
对 108 例晚期 NSCLC 患者的福尔马林固定、石蜡包埋（FFPE）样本进行了基于 nCounter 的检测，并将结果与 FISH、IHC 和逆转录 PCR（RT-PCR）进行了比较。在 29 例患者的亚组中回顾性收集了关于融合激酶抑制剂反应的数据。
在 108 例 FFPE 样本中，98 例成功地通过 nCounter 进行了分析（91%），其中鉴定出 55 例融合阳性病例（32 例、21 例和 2 例）。nCounter 结果与 ALK 的 IHC 高度一致（98.5%，CI=91.8-99.7），而与 FISH 相比，有 11 个差异（87.5%的一致性，CI=79.0-92.9）。对于，nCounter 与 IHC 和 FISH 的一致性相似（87.2%和 85.9%），但大量样本仅通过 1 种或 2 种技术呈阳性。在从融合激酶抑制剂中获得临床获益的 25 例患者中，24 例患者 nCounter 阳性，22 例患者 FISH 阳性。
nCounter 与 IHC 和 FISH 相比具有优势，可用于鉴定晚期 NSCLC 中存在 // 融合基因的患者。
