Background: In our recent study, of cases positive for epidermal growth factor receptor (EGFR) exon 19 deletions using comprehensive genomic profiling (CGP), 17/77 (22%) patients with prior standard of care (SOC) EGFR testing results available were previously negative for exon 19 deletion. Our aim was to compare the detection rates of CGP versus SOC testing for well-characterized sensitizing EGFR point mutations (pm) in our 6,832-patient cohort.
Materials and methods: DNA was extracted from 40 microns of formalin-fixed paraffin-embedded sections from 6,832 consecutive cases of non-small cell lung cancer (NSCLC) of various histologies (2012-2015). CGP was performed using a hybrid capture, adaptor ligation-based next-generation sequencing assay to a mean coverage depth of 576×. Genomic alterations (pm, small indels, copy number changes and rearrangements) involving EGFR were recorded for each case and compared with prior testing results if available.
Results: Overall, there were 482 instances of EGFR exon 21 L858R (359) and L861Q (20), exon 18 G719X (73) and exon 20 S768I (30) pm, of which 103 unique cases had prior EGFR testing results that were available for review. Of these 103 cases, CGP identified 22 patients (21%) with sensitizing EGFR pm that were not detected by SOC testing, including 9/75 (12%) patients with L858R, 4/7 (57%) patients with L861Q, 8/20 (40%) patients with G719X, and 4/7 (57%) patients with S768I pm (some patients had multiple EGFR pm). In cases with available clinical data, benefit from small molecule inhibitor therapy was observed.
Conclusion: CGP, even when applied to low tumor purity clinical-grade specimens, can detect well-known EGFR pm in NSCLC patients that would otherwise not be detected by SOC testing. Taken together with EGFR exon 19 deletions, over 20% of patients who are positive for EGFR-activating mutations using CGP are previously negative by SOC EGFR mutation testing, suggesting that thousands of such patients per year in the U.S. alone could experience improved clinical outcomes when hybrid capture-based CGP is used to inform therapeutic decisions.
Implications for practice: This study points out that genomic profiling, as based on hybrid capture next-generation sequencing, can identify lung cancer patients with point mutation in epidermal growth factor receptor (EGFR) missed by standard molecular testing who can likely benefit from anti-EGFR targeted therapy. Beyond the specific findings regarding false-negative point mutation testing for EGFR, this study highlights the need for oncologists and pathologists to be cognizant of the performance characteristics of testing deployed and the importance of clinical intuition in questioning the results of laboratory testing.
摘要
背景.在我们的近期研究中,在使用综合基因组分析(CGP)确定表皮生长因子受体(EGFR)外显子19缺失检测呈阳性的病例中,17/77例(22%)可提供既往标准诊疗(SOC)EGFR检测结果的患者先前的外显子19缺失检测呈阴性。我们的目的是在我们的6 832例患者队列中比较CGP与SOC检测对良好表征的敏感性EGFR点突变(pm)的检出率。
材料和方法.DNA提取自6 832例组织学特征不同的非小细胞肺癌(NSCLC)连续病例(2012‐2015年)的40微米福尔马林固定、石蜡包埋切片。采用杂交捕获适配体连接性下一代测序分析执行CGP,平均覆盖深度为576 X。记录了各病例中涉及EGFR的基因组改变(pm、小片段插入缺失、拷贝数改变和重排)并将之与既往检测结果进行比较(如可用)。
结果.总体而言,有482例EGFR外显子21 L858R (359)和L861Q (20)、外显子18 G719X (73)和外显子20 S768I (30) pm,其中103例独特病例具有可供审查的既往EGFR检测结果。在上述103例病例中,CGP识别出22例(21%)存在敏感性EGFR pm(未通过SOC检测检出)的患者,包括9/75例(12%)存在L858R的患者、4/7例(57%)存在L861Q的患者、8/20例(40%)存在G719X的患者和4/7例(57%)存在S768I pm的患者(某些患者存在多重EGFR pm)。在具有可用临床数据的病历中,观察到小分子抑制剂疗法的获益。
结论.即使在低肿瘤纯度临床级标本,CGP也可在NSCLC患者中检测到知名的EGFR pm(未能通过SOC检测检出)。结合EGFR外显子19缺失,在使用CGP得出的EGFR激活突变结果为阳性的患者中,超过20%的患者先前通过SOC EGFR突变检测得出的结果为阴性,表明仅在美国每年就有数千名该等患者可在使用杂交捕获性CGP改变治疗决策并出现临床结果改善。
对临床实践的提示:本研究指出基因组分析(基于杂交捕获的下一代测序)可识别出通过标准分子检测未检出存在表皮生长因子受体(EGFR)点突变的肺癌患者,该等患者可能会从抗EGFR靶向治疗中获益。除关于EGFR假阴性点突变检测的特定发现外,本研究强调肿瘤医师和病理学家需要认识到所开展检测的性能特征以及临床直觉在质疑实验室检测结果方面的重要性。
Keywords: Comprehensive genomic profiling; Epidermal growth factor receptor point mutations; Hybrid capture.
© AlphaMed Press 2018.