PO.CL01.11 · 临床研究
应用肿瘤知情ctDNA分析监测结直肠癌的分子残留疾病
Monitoring molecular residual disease in colorectal cancer using tumor-informed ctDNA analysis
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
背景：循环肿瘤DNA（ctDNA）已成为检测分子残留疾病（MRD）和预测结直肠癌（CRC）复发的关键工具。肿瘤知情ctDNA检测依赖于来自肿瘤组织的参考突变谱，通常源自福尔马林固定石蜡包埋（FFPE）或新鲜冷冻（FF）样本。尽管FFPE组织广泛可得，但其易受福尔马林诱导的伪影影响，可能影响突变判定的准确性。本研究评估了ctDNA MRD检测的灵敏度和特异度，比较了FFPE与FF组织之间的突变谱和ctDNA MRD性能，并评估了ctDNA的预后价值。
方法：我们分析了28例接受根治性手术的CRC患者。对18例FFPE和16例FF肿瘤样本（包括六对配对样本）进行全基因组测序，以评估变异负荷、等位基因频率和突变特征。采用串联纠错测序平台（AccuScan）在术前和术后测定血浆ctDNA。复发的性能指标在标志性时间点（术后2-6周）和纵向随访期间进行评估。无病生存期（DFS）采用Kaplan-Meier方法分析。
结果：FFPE样本的中位变异计数高于FF组织（8,774 vs. 4,906，p = 0.001），变异等位基因频率较低（17.54% vs. 21.38%，p = 0.033），并富集A>T颠换（p = 0.031）。尽管存在这些差异，ctDNA MRD检测在各类组织中对复发均显示100%特异度和阳性预测值。FFPE知情检测在纵向监测中显示更高灵敏度（88.9% vs. 71.4%）。MRD阳性与DFS缩短强相关（p < 0.0001）。在两个病例中，FFPE知情检测检出的复发被FF分析漏检，提示FF样本可能存在假阴性。
讨论：这些发现支持FFPE组织尽管伪影较多，但经生物信息学处理后是ctDNA MRD检测在临床上实用且往往更灵敏的来源。ctDNA的高特异度凸显了其在指导治疗决策方面的效用。本研究证实了ctDNA的预后价值，并倡导使用存档FFPE组织以提高检测可及性而不影响准确性，从而促进液体活检整合入个体化CRC管理。
查看英文原文 English abstract
Background: Circulating tumor DNA (ctDNA) has become a critical tool for detecting molecular residual disease (MRD) and predicting recurrence in colorectal cancer (CRC). Tumor-informed ctDNA assays depend on a reference mutation profile from tumor tissue, commonly sourced from formalin-fixed, paraffin-embedded (FFPE) or fresh-frozen (FF) samples. Although FFPE tissues are widely available, they are susceptible to formalin-induced artifacts that may affect mutation calling accuracy. This study evaluated the sensitivity and specificity of ctDNA MRD assays, compared the mutation profiles and ctDNA MRD performance between FFPE and FF tissues, and evaluated the prognostic value of ctDNA.
Methods: We analyzed 28 CRC patients after curative-intent surgery. Whole-genome sequencing of 18 FFPE and 16 FF tumor samples (including six matched pairs) was conducted to assess variant burden, allele frequency, and mutational signatures. Plasma ctDNA was measured pre- and post-operatively using the tandem error-correction sequencing platform (AccuScan). Performance metrics for recurrence were evaluated at a landmark period (2-6 weeks post-surgery) and during longitudinal follow-up. Disease-free survival (DFS) was analyzed with Kaplan-Meier methods.
Results: FFPE samples exhibited a higher median variant count than FF tissues (8,774 vs. 4,906, p = 0.001) and lower variant allele frequency (17.54% vs. 21.38%, p = 0.033), along with enriched A>T transversions ( p = 0.031). Despite these differences, ctDNA MRD detection showed 100% specificity and positive predictive value for recurrence across tissue types. FFPE-informed testing showed higher sensitivity during longitudinal monitoring (88.9% vs. 71.4%). MRD positivity was strongly associated with reduced DFS ( p < 0.0001). In two cases, recurrence detected by FFPE-informed testing was missed with FF-based analysis, suggesting potential false negatives with FF samples.
Discussion: These findings support that FFPE tissues, despite more artifacts, are a clinically practical and often more sensitive source for ctDNA MRD assays after bioinformatic processing. The high specificity of ctDNA underscores its utility in guiding treatment decisions. This study confirms the prognostic value of ctDNA and promotes the use of archival FFPE tissues to improve test accessibility without compromising accuracy, facilitating the integration of liquid biopsy into personalized CRC management.
利益披露 Disclosure
W. C. Cho, None.
Q. Yao,
AccuraGen Inc. Employment.
Y. Wang,
AccuraGen Inc. Employment.
T. Berntsen,
AccuraGen Inc. Employment.
G. Yeung,
AccuraGen Inc. Employment.
P. Tang,
AccuraGen Inc. Employment.
T. Wittkop,
AccuraGen Inc. Employment.
L. Weng,
AccuraGen Inc. Employment.
L. Ng, None..
D. C. Foo, None.