BackgroundAs circulating tumour DNA (ctDNA) liquid biopsy analysis is increasingly incorporated into modern oncological practice, establishing the impact of genomic intra-tumoural heterogeneity (ITH) upon data output is paramount. Despite advances in other cancer types the evidence base in head and neck squamous cell carcinoma (HNSCC) remains poor. We sought to investigate the utility of ctDNA to detect ITH in HNSCC.MethodsIn a pilot cohort of 9 treatment-naïve HNSCC patients, DNA from two intra-tumoural sites (core and margin) was whole-exome sequenced. A 9-gene panel was designed to perform targeted sequencing on pre-treatment plasma cell-free DNA and selected post-treatment samples.ResultsRates of genomic ITH among the 9 patients was high. COSMIC variants from 19 TCGA HNSCC genes demonstrated an 86.9% heterogeneity rate (present in one tumour sub-site only). Across all patients, cell-free DNA (ctDNA) identified 12.9% (range 7.5-19.8%) of tumour-specific variants, of which 55.6% were specific to a single tumour sub-site only. CtDNA identified 79.0% (range: 55.6-90.9%) of high-frequency variants (tumour VAF>5%). Analysis of ctDNA in serial post-treatment blood samples in patients who suffered recurrence demonstrated dynamic changes in both tumour-specific and acquired variants that predicted recurrence ahead of clinical detection.ConclusionWe demonstrate that a ctDNA liquid biopsy identified spatial genomic ITH in HNSCC and reliably detected high-frequency driver mutations. Serial sampling allowed post-treatment surveillance and early identification of treatment failure.

中文翻译：

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循环肿瘤 DNA 检测导致头颈鳞状细胞癌肿瘤内空间和时间异质性的体细胞变异

背景随着循环肿瘤 DNA (ctDNA) 液体活检分析越来越多地融入现代肿瘤学实践，确定基因组肿瘤内异质性 (ITH) 对数据输出的影响至关重要。尽管其他癌症类型取得了进展，但头颈鳞状细胞癌（HNSCC）的证据基础仍然很薄弱。我们试图研究 ctDNA 在 HNSCC 中检测 ITH 的效用。方法在 9 名初治 HNSCC 患者的试点队列中，对两个肿瘤内位点（核心和边缘）的 DNA 进行全外显子组测序。设计9基因panel对治疗前血浆游离DNA和选定的治疗后样本进行靶向测序。结果9例患者中基因组ITH率较高。 19 个 TCGA HNSCC 基因的 COSMIC 变异表现出 86.9% 的异质性（仅存在于一个肿瘤亚位点）。在所有患者中，游离 DNA (ctDNA) 鉴定出 12.9%（范围 7.5-19.8%）的肿瘤特异性变异，其中 55.6% 仅针对单个肿瘤亚位点。 CtDNA鉴定了79.0％(范围：55.6-90.9％)的高频变异(肿瘤VAF＞5％)。对复发患者连续治疗后血液样本中的 ctDNA 分析表明，肿瘤特异性变异和获得性变异的动态变化可在临床检测之前预测复发。结论我们证明，ctDNA 液体活检识别了 HNSCC 中的空间基因组 ITH，并可靠地检测到高频驱动突变。连续采样可以进行治疗后监测并及早发现治疗失败。