Glioma-derived cell-free DNA (cfDNA) is challenging to detect using liquid biopsy because quantities in body fluids are low. We determined the glioma-derived DNA fraction in cerebrospinal fluid (CSF), plasma, and urine samples from patients using sequencing of personalized capture panels guided by analysis of matched tumor biopsies. By sequencing cfDNA across thousands of mutations, identified individually in each patient’s tumor, we detected tumor-derived DNA in the majority of CSF (7/8), plasma (10/12), and urine samples (10/16), with a median tumor fraction of 6.4 × 10⁻³, 3.1 × 10⁻⁵, and 4.7 × 10⁻⁵, respectively. We identified a shift in the size distribution of tumor-derived cfDNA fragments in these body fluids. We further analyzed cfDNA fragment sizes using whole-genome sequencing, in urine samples from 35 glioma patients, 27 individuals with non-malignant brain disorders, and 26 healthy individuals. cfDNA in urine of glioma patients was significantly more fragmented compared to urine from patients with non-malignant brain disorders (P = 1.7 × 10⁻²) and healthy individuals (P = 5.2 × 10⁻⁹). Machine learning models integrating fragment length could differentiate urine samples from glioma patients (AUC = 0.80–0.91) suggesting possibilities for truly non-invasive cancer detection.

中文翻译：

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神经胶质瘤患者尿液和血浆中游离 DNA 的断裂模式和个性化测序


由于体液中的数量很少，因此使用液体活检检测胶质瘤来源的游离 DNA (cfDNA) 具有挑战性。我们通过匹配肿瘤活检分析指导下的个性化捕获组测序，确定了患者脑脊液 (CSF)、血浆和尿液样本中胶质瘤来源的 DNA 分数。通过对每个患者肿瘤中单独鉴定的数千个突变进行 cfDNA 测序，我们在大多数脑脊液 (7/8)、血浆 (10/12) 和尿液样本 (10/16) 中检测到了肿瘤衍生的 DNA，其中中位肿瘤分数分别为 6.4 × 10 ^-3 、3.1 × 10 ^-5和 4.7 × 10 ^-5 。我们发现这些体液中肿瘤来源的 cfDNA 片段的大小分布发生了变化。我们使用全基因组测序进一步分析了 35 名神经胶质瘤患者、27 名非恶性脑部疾病患者和 26 名健康个体的尿液样本中的 cfDNA 片段大小。与非恶性脑部疾病患者 ( P = 1.7 × 10 ^-2 ) 和健康个体 ( P = 5.2 × 10 ^-9 ) 的尿液相比，神经胶质瘤患者尿液中的 cfDNA 明显更加碎片化。整合片段长度的机器学习模型可以区分来自神经胶质瘤患者的尿液样本（AUC = 0.80-0.91），这表明真正的非侵入性癌症检测的可能性。