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High-Throughput Diagnostic Profiling of Clinically Actionable Gene Fusions in Lung Cancer

机译：肺癌临床上可操作基因融合的高通量诊断分析

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Molecular profiling of non-small cell lung cancers (NSCLC) has a strong impact on clinical decision making and current oncological therapies. Besides detection of activating mutations in EGFR, analysis of ALK and ROS1 gene rearrangements has come into focus for targeted therapies. Targeted massive parallel sequencing (MPS) has been established for routine diagnostic profiling of the most prevalent oncogenic mutations in NSCLC, but not for the detection of gene rearrangements yet. Here, we present and evaluate an MPS-based panel sequencing approach which simultaneously detects ALK, ROS1, and RET fusions as well as somatic mutations in a single multiplex assay using formalin-fixed paraffin-embedded (FFPE) tissue. To this end, we first evaluated sensitivity and specificity of the fusion assay retrospectively by employing it to a set of 50 NSCLC with known gene fusions (n = 535) and with no gene fusions (n = 515). The sensitivity and specificity of the MPS assay for the detection of known fusions was 100%. In a second prospective phase, we implemented the approach of parallel mutation and gene fusion detection in our routine diagnostic workflow to assess performance of the test in a diagnostic outreach setting. Our prospective screening of 109 NSCLC samples revealed four gene fusions all of which were confirmed by FISH. In conclusion, our approach facilitates simultaneous high-throughput detection of gene fusions and somatic mutations in NSCLC samples and is able to replace conventional methods. (c) 2015 Wiley Periodicals, Inc.
机译：非小细胞肺癌（NSCLC）的分子谱分析对临床决策和当前的肿瘤治疗具有重要影响。除了检测EGFR中的激活突变外，ALK和ROS1基因重排的分析已成为靶向治疗的重点。靶向大规模并行测序（MPS）已建立用于NSCLC中最普遍的致癌突变的常规诊断分析，但尚未用于检测基因重排。在这里，我们介绍并评估一种基于MPS的面板测序方法，该方法可在使用福尔马林固定石蜡包埋（FFPE）的单次多重测定中同时检测ALK，ROS1和RET融合以及体细胞突变。为此，我们首先回顾性地评估了融合测定的敏感性和特异性，方法是将其用于一组50个具有已知基因融合（n = 535）和无基因融合（n = 515）的NSCLC。用于检测已知融合蛋白的MPS分析的灵敏度和特异性为100％。在第二个预期阶段，我们在常规诊断工作流程中实施了平行突变和基因融合检测的方法，以评估在诊断外展环境中测试的性能。我们对109例NSCLC样本进行了前瞻性筛选，结果发现了4种基因融合体，所有这些融合体均已被FISH证实。总之，我们的方法有助于同时高通量检测NSCLC样品中的基因融合和体细胞突变，并能够替代传统方法。 （c）2015年威利期刊有限公司

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