PDF(Pubmed)
Abstract：
Circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) detection, which can identify disease relapse ahead of radiological imaging, has shown promising performance. The objective of this study was to develop and validate OriMIRACLE S (Minimal Residual Circulating Nucleic Acid Longitudinal Detection in Solid Tumor), a highly sensitive and specific tumor-informed assay for MRD detection.
Tumor-specific somatic single nucleotide variants (SNVs) were identified via whole exome sequencing of tumor tissue and matched germline DNA. Clonal SNVs were selected using the OriSelector algorithm for patient-specific, multiplex PCR-based NGS assays in MRD detection. Plasma-free DNA from patients with gastrointestinal tumors prior to and following an operation, and during monitoring, were ultradeep sequenced.
The detection of three positive sites was sufficient to achieve nearly 100% overall sample level sensitivity and specificity and was determined by calculating binomial probability based on customized panels containing 21 to 30 variants. A total of 127 patients with gastrointestinal tumors were enrolled in our study. Preoperatively, MRD was positive in 18 of 26 patients (69.23%). Following surgery, MRD was positive in 24 of 82 patients (29.27%). The positivity rate for MRD was 33.33% (n = 18) for gastric adenocarcinoma and 32.26% (n = 62) for colorectal cancer. Twenty (20) of 59 patients (34.48%) experienced a change in MRD status over the monitoring period. Patients 8 and 31 responded to 3 cycles of systemic therapy, after which levels for all ctDNA dropped below the detection limit. Patient 53 was an example of using MRD to predict tumor metastasis. Patient 55 showed a weak response to treatments first and respond to new systemic therapy after tumor progression.
Our study identified a sensitive and specific clinical detection method for low frequency ctDNA, and explored the detection performance of this technology in gastrointestinal tumors.
Tumor-specific somatic single nucleotide variants (SNVs) were identified via whole exome sequencing of tumor tissue and matched germline DNA. Clonal SNVs were selected using the OriSelector algorithm for patient-specific, multiplex PCR-based NGS assays in MRD detection. Plasma-free DNA from patients with gastrointestinal tumors prior to and following an operation, and during monitoring, were ultradeep sequenced.
The detection of three positive sites was sufficient to achieve nearly 100% overall sample level sensitivity and specificity and was determined by calculating binomial probability based on customized panels containing 21 to 30 variants. A total of 127 patients with gastrointestinal tumors were enrolled in our study. Preoperatively, MRD was positive in 18 of 26 patients (69.23%). Following surgery, MRD was positive in 24 of 82 patients (29.27%). The positivity rate for MRD was 33.33% (n = 18) for gastric adenocarcinoma and 32.26% (n = 62) for colorectal cancer. Twenty (20) of 59 patients (34.48%) experienced a change in MRD status over the monitoring period. Patients 8 and 31 responded to 3 cycles of systemic therapy, after which levels for all ctDNA dropped below the detection limit. Patient 53 was an example of using MRD to predict tumor metastasis. Patient 55 showed a weak response to treatments first and respond to new systemic therapy after tumor progression.
Our study identified a sensitive and specific clinical detection method for low frequency ctDNA, and explored the detection performance of this technology in gastrointestinal tumors.
摘要：
背景：基于循环肿瘤DNA（ctDNA）的微小残留病（MRD）检测，可以在放射成像之前识别疾病复发，表现出了有希望的表现。本研究的目的是开发和验证OriMIRACLES（实体瘤中最小残留循环核酸纵向检测），用于MRD检测的高度敏感和特异性的肿瘤信息测定。
方法：通过肿瘤组织和匹配种系DNA的全外显子组测序鉴定肿瘤特异性体细胞单核苷酸变体（SNV）。使用Oriselector算法选择克隆SNV，用于患者特异性，MRD检测中基于多重PCR的NGS检测。手术前后胃肠道肿瘤患者的无血浆DNA，在监测过程中，进行了超深测序。
结果:三个阳性位点的检测足以实现几乎100%的总体样品水平灵敏度和特异性,并且通过基于包含21至30个变体的定制组计算二项概率来确定。我们的研究共纳入了127例胃肠道肿瘤患者。术前,26例患者中有18例MRD阳性（69.23%）。手术后,82例患者中24例MRD呈阳性（29.27%）。胃腺癌的MRD阳性率为33.33%(n=18)，结直肠癌的MRD阳性率为32.26%(n=62)。59名患者中的20名(34.48%)在监测期间经历了MRD状态的改变。患者8和31对3个周期的全身治疗有反应，之后，所有ctDNA的水平都下降到检测极限以下。患者53是使用MRD预测肿瘤转移的实例。患者55首先表现出对治疗的弱反应,并且在肿瘤进展后对新的全身治疗有反应。
结论：我们的研究确定了一种敏感和特异的低频ctDNA临床检测方法，探讨了该技术在胃肠道肿瘤中的检测性能。
方法：通过肿瘤组织和匹配种系DNA的全外显子组测序鉴定肿瘤特异性体细胞单核苷酸变体（SNV）。使用Oriselector算法选择克隆SNV，用于患者特异性，MRD检测中基于多重PCR的NGS检测。手术前后胃肠道肿瘤患者的无血浆DNA，在监测过程中，进行了超深测序。
结果:三个阳性位点的检测足以实现几乎100%的总体样品水平灵敏度和特异性,并且通过基于包含21至30个变体的定制组计算二项概率来确定。我们的研究共纳入了127例胃肠道肿瘤患者。术前,26例患者中有18例MRD阳性（69.23%）。手术后,82例患者中24例MRD呈阳性（29.27%）。胃腺癌的MRD阳性率为33.33%(n=18)，结直肠癌的MRD阳性率为32.26%(n=62)。59名患者中的20名(34.48%)在监测期间经历了MRD状态的改变。患者8和31对3个周期的全身治疗有反应，之后，所有ctDNA的水平都下降到检测极限以下。患者53是使用MRD预测肿瘤转移的实例。患者55首先表现出对治疗的弱反应,并且在肿瘤进展后对新的全身治疗有反应。
结论：我们的研究确定了一种敏感和特异的低频ctDNA临床检测方法，探讨了该技术在胃肠道肿瘤中的检测性能。
