Bontoux Christophe, Lacoux Caroline, Benzaquen Jonathan, Boutros Jacques, Rignol Guylène, Long-Mira Elodie, Lassalle Sandra, Allegra Maryline, Bohly Doriane, Garcia Mathieu, Bonnetaud Christelle, Bordone Olivier, Félix Jean-Marc, Lespinet-Fabre Virginie, Tanga Virginie, Marquette Charles-Hugo, Taly Valérie, Baurès Aurélia, Heeke Simon, Ilié Marius, Hofman Véronique, Hofman Paul
Department of Pathology, Cancer University Institute of Toulouse-Oncopole, University Hospital of Toulouse, Toulouse, 31059, France.
OncoSarc, INSERM U1037, Cancer Research Center in Toulouse, Toulouse, 31000, France.
J Exp Clin Cancer Res. 2025 Aug 6;44(1):229. doi: 10.1186/s13046-025-03480-x.
Liquid biopsies (LB) are used increasingly to detect actionable mutations in patients newly diagnosed with advanced non-small cell lung cancer (aNSCLC), though tissue biopsies (TB) still remain the gold standard. The value of systematically combining LB and TB next-generation sequencing (NGS) for genomic profiling in these patients remains controversial.
This single-centre retrospective study included 102 matched TB and LB samples collected from aNSCLC patients at diagnosis. Four circulating free DNA (cfDNA)-based NGS assays (1-4) were compared on site for performance and concordance with TB to detect ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) I/II. Additionally, cfDNA droplet digital PCR methylation (ddPCR-met) testing estimated the tumour fraction to refine the interpretation of wild-type (WT) results.
Out of 102 patients, 13% had stage IIIB disease, and 11% presented with brain-only metastases. Adenocarcinoma was the predominant subtype (84%). Ninety LB samples yielded interpretable results across the four assays. Positive percent agreement with TB ranged from 56% (assay 2) to 79% (assay 4), with high concordance, particularly for single-nucleotide variants (SNVs). Hybrid capture-based assays (3 and 4) detected eight and seven gene fusions, respectively, while amplicon-based assays (1 and 2) detected only two each. Assay 3 only identified 12 MET amplifications, five of which were confirmed by fluorescence in situ hybridisation (FISH) but were missed by TB-based NGS. Five out of six negative cfDNA samples with ddPCR-met testing were WT across all assays. The plasma-first approach added incremental value, up to 21% (assay 3). Amplicon-based assays were faster and required less input of DNA for analysis. Patients with stage IIIB or brain-only metastases were significantly more likely to have negative/low levels of cfDNA ddPCR-met.
LB-based NGS demonstrated high concordance with TB in newly diagnosed aNSCLC, particularly for detection of SNV. Hybrid capture assays showed superior performance in identifying gene fusions and MET amplifications. The incremental value of a plasma-first strategy was limited in this real-life study. Thus, LB-based NGS on site should be seen as a complementary tool to TB-based NGS or an alternative when tissue samples are unavailable. Additionally, cfDNA methylation analysis enhances diagnostic accuracy in specific cases.
液体活检（LB）越来越多地用于检测新诊断的晚期非小细胞肺癌（aNSCLC）患者的可操作突变，尽管组织活检（TB）仍然是金标准。在这些患者中，系统地结合LB和TB下一代测序（NGS）进行基因组分析的价值仍存在争议。
这项单中心回顾性研究纳入了102对在诊断时从aNSCLC患者收集的匹配的TB和LB样本。对四种基于循环游离DNA（cfDNA）的NGS检测方法（1-4）进行了现场性能比较，并与TB检测ESMO分子靶点临床可操作性量表（ESCAT）I/II的一致性进行了比较。此外，cfDNA液滴数字PCR甲基化（ddPCR-met）检测估计肿瘤分数，以完善对野生型（WT）结果的解释。
102例患者中，13%患有IIIB期疾病，11%仅出现脑转移。腺癌是主要亚型（84%）。90份LB样本在四种检测方法中均产生了可解释的结果。与TB的阳性百分比一致性范围为56%（检测方法2）至79%（检测方法4），一致性较高，尤其是对于单核苷酸变异（SNV）。基于杂交捕获的检测方法（3和4）分别检测到8个和7个基因融合，而基于扩增子的检测方法（1和2）各仅检测到2个。检测方法3仅鉴定出12个MET扩增，其中5个通过荧光原位杂交（FISH）得到证实，但基于TB的NGS未检测到。ddPCR-met检测的6个cfDNA阴性样本中有5个在所有检测方法中均为WT。血浆优先方法增加了高达21%（检测方法3）的附加值。基于扩增子的检测方法速度更快，分析所需的DNA输入量更少。IIIB期或仅脑转移的患者cfDNA ddPCR-met呈阴性/低水平的可能性显著更高。
基于LB的NGS在新诊断的aNSCLC中与TB具有高度一致性，尤其是在检测SNV方面。杂交捕获检测方法在鉴定基因融合和MET扩增方面表现出卓越性能。在这项真实世界研究中，血浆优先策略的附加值有限。因此，现场基于LB的NGS应被视为基于TB的NGS的补充工具，或在无法获得组织样本时的替代方法。此外，cfDNA甲基化分析可提高特定病例的诊断准确性。
