Validating a targeted next-generation sequencing assay and profiling somatic variants in Chinese non-small cell lung cancer patients
Validating a targeted next-generation sequencing assay and profiling somatic variants in Chinese non-small cell lung cancer patients
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DOI：
10.1038/s41598-020-58819-5
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发表时间：
2020-02-07
影响因子：
4.6
通讯作者：
Ye, Feng
中科院分区：
文献类型：
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作者：
Jiang, Ruirui;Zhang, Bo;Ye, Feng
非小细胞肺癌（NSCLC）是一种以复杂的基因组改变为特征的肿瘤。因此，对大型NSCLC患者队列进行分子分析是精准医疗的先决条件。我们首先验证了下一代测序（NGS）癌症热点面板OncoAim在福尔马林固定石蜡包埋（FFPE）样本上的检测性能。然后，我们利用OncoAim来描述中国NSCLC患者的基因组畸变。对于等位基因频率（MAF）>= 5%的突变，在>500 x覆盖深度时，总体检测性能是强大的，灵敏度>99%，特异性高（阳性预测值> 99%），准确性94%，重复性96%。分析422例NSCLC FFPE样本显示，患者特征，包括性别、年龄、淋巴转移、组织学分级和组织学亚型与EGFR和TP53突变发生率显著相关。此外，RTK信号通路激活在腺癌中富集，而PI（3）K通路激活、氧化应激通路激活和TP53通路抑制在鳞状细胞癌中更普遍。此外，新的共存（例如，BRAF和PTEN的变体）和相互排斥（例如，最后，我们揭示了TP53中不同的突变谱，以及先前被低估的PTEN畸变。我们的研究结果有助于提高中国NSCLC患者的诊断，预后和个性化治疗决策。
Non-small cell lung cancer (NSCLC) is featured with complex genomic alterations. Molecular profiling of large cohort of NSCLC patients is thus a prerequisite for precision medicine. We first validated the detection performance of a next-generation sequencing (NGS) cancer hotspot panel, OncoAim, on formalin-fixed paraffin-embedded (FFPE) samples. We then utilized OncoAim to delineate the genomic aberrations in Chinese NSCLC patients. Overall detection performance was powerful for mutations with allele frequency (MAF) >= 5% at >500 x coverage depth, with >99% sensitivity, high specificity (positive predictive value > 99%), 94% accuracy and 96% repeatability. Profiling 422 NSCLC FFPE samples revealed that patient characteristics, including gender, age, lymphatic spread, histologic grade and histologic subtype were significantly associated with the mutation incidence of EGFR and TP53. Moreover, RTK signaling pathway activation was enriched in adenocarcinoma, while PI(3)K pathway activation, oxidative stress pathway activation, and TP53 pathway inhibition were more prevalent in squamous cell carcinoma. Additionally, novel co-existence (e.g., variants in BRAF and PTEN) and mutual-exclusiveness (e.g., alterations in EGFR and NFE2L2) were found. Finally, we revealed distinct mutation spectrum in TP53, as well as a previously undervalued PTEN aberration. Our findings could aid in improving diagnosis, prognosis and personalized therapeutic decisions of Chinese NSCLC patients.