Xu Jianping, Pu Yue, Lin Rui, Xiao Shanshan, Fu Yingxue, Wang Tao
Department of Medical Oncology, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China.
Peking Union Medical College, Beijing, China.
Front Med (Lausanne). 2022 Mar 3;9:822200. doi: 10.3389/fmed.2022.822200. eCollection 2022.
Circulating tumor DNA (ctDNA), a tumor-derived fraction of cell-free DNA (cfDNA), has emerged as a promising marker in targeted therapy, immunotherapy, and minimal residual disease (MRD) monitoring in postsurgical patients. However, ctDNA level in early-stage cancers and postsurgical patients is very low, which posed many technical challenges to improve the detection rate and sensitivity, especially in the clinical practice of MRD detection. These challenges usually include insufficient DNA input amount, limit of detection (LOD), and high experimental costs. To resolve these challenges, we developed an ultrasensitive ctDNA MRD detection system in this study, namely PErsonalized Analysis of Cancer (PEAC), to simultaneously detect up to 37 mutations, which account for 70-80% non-small cell lung cancer (NSCLC) driver mutations from low plasma sample volume and enables LOD of 0.01% at a single-site level. We demonstrated the high performance achieved by PEAC on both cfDNA reference standards and clinical plasma samples from three NSCLC patient cohorts. For cfDNA reference standards, PEAC achieved a specificity of 99% and a sensitivity of 87% for the mutations at 0.01% allele fraction. In the second cohort, PEAC showed 100% concordance rate between ddPCR and Next-generation sequencing (NGS) among 29 samples. In the third cohort, 22 of 59 patients received EGFR TKI treatment. Among them, three in four patients identified low level actionable gene mutations only by PEAC had partial responses after targeted therapy, demonstrating high ctDNA detection ability of PEAC. Overall, the developed PEAC system can detect the majority of NSCLC driver mutations using 8-10 ml plasma samples, and has the advantages of high detection sensitivity and lower costs compared with the existing technologies such as ddPCR and NGS. These advantages make the PEAC system quite appropriate for ctDNA and MRD detection in early-stage NSCLC and postsurgical recurrence monitoring.
循环肿瘤DNA（ctDNA）是游离DNA（cfDNA）的肿瘤衍生部分，已成为靶向治疗、免疫治疗以及术后患者微小残留病（MRD）监测中有前景的标志物。然而，早期癌症和术后患者的ctDNA水平非常低，这给提高检测率和灵敏度带来了诸多技术挑战，尤其是在MRD检测的临床实践中。这些挑战通常包括DNA输入量不足、检测限（LOD）以及高昂的实验成本。为解决这些挑战，我们在本研究中开发了一种超灵敏的ctDNA MRD检测系统，即癌症个性化分析（PEAC），可同时检测多达37种突变，这些突变占非小细胞肺癌（NSCLC）驱动突变的70 - 80%，能从少量血浆样本中检测到，并且在单位点水平实现0.01%的检测限。我们展示了PEAC在cfDNA参考标准品和来自三个NSCLC患者队列的临床血浆样本上所取得的高性能。对于cfDNA参考标准品，PEAC在等位基因分数为0.01%时，对突变的特异性达到99%，灵敏度为87%。在第二个队列中，PEAC在29个样本中显示出ddPCR与二代测序（NGS）之间100%的一致性率。在第三个队列中，59名患者中有22名接受了EGFR TKI治疗。其中，仅通过PEAC检测出低水平可操作基因突变的患者中有四分之三在靶向治疗后出现部分缓解，证明了PEAC具有高ctDNA检测能力。总体而言，所开发的PEAC系统使用8 - 10毫升血浆样本就能检测出大多数NSCLC驱动突变，与ddPCR和NGS等现有技术相比，具有检测灵敏度高和成本较低的优势。这些优势使得PEAC系统非常适合早期NSCLC的ctDNA和MRD检测以及术后复发监测。
