Purpose: Although cell-free DNA (cfDNA) testing is expected to drive cancer precision medicine, little is known about the significance of detecting low-frequency variants in circulating cell-free tumor DNA (ctDNA) in castration-resistant prostate cancer (CRPC). We aimed to identify genomic profile including low-frequency variants in ctDNA from patients with CRPC and investigate the clinical utility of detecting variants with variant allele frequency (VAF) below 1%. Experimental Design: This prospective, multicenter cohort study enrolled patients with CRPC eligible for treatment with abiraterone or enzalutamide. We performed targeted sequencing of pretreatment cfDNA and paired leukocyte DNA with molecular barcodes, and ctDNA variants with a VAF ≥0.1% were detected using an in-house pipeline. We investigated progression-free survival (PFS) and overall survival (OS) after different ctDNA fraction cutoffs were applied. Results: One hundred patients were analyzed (median follow-up 10.7 months). We detected deleterious ATM , BRCA2 , and TP53 variants even in samples with ctDNA fraction below 2%. When the ctDNA fraction cutoff value of 0.4% was applied, significant differences in PFS and OS were found between patients with and without defects in ATM or BRCA2 [HR, 2.52; 95% confidence interval (CI), 1.24–5.11; P = 0.0091] and TP53 (HR, 3.74; 95% CI, 1.60–8.71; P = 0.0014). However, these differences were no longer observed when the ctDNA fraction cutoff value of 2% was applied, and approximately 50% of the samples were classified as ctDNA unquantifiable. Conclusions: Detecting low-frequency ctDNA variants with a VAF <1% is important to identify clinically informative genomic alterations in CRPC.

中文翻译：

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检测游离 DNA 低频变异对去势抵抗性前列腺癌治疗的临床影响

目的：尽管无细胞 DNA (cfDNA) 检测有望推动癌症精准医疗，但人们对检测去势抵抗性前列腺癌 (CRPC) 循环游离细胞肿瘤 DNA (ctDNA) 中的低频变异的意义知之甚少. 我们旨在鉴定 CRPC 患者的基因组谱，包括 ctDNA 中的低频变异，并研究检测变异等位基因频率 (VAF) 低于 1% 的变异的临床效用。实验设计：这项前瞻性、多中心队列研究招募了符合阿比特龙或恩杂鲁胺治疗的 CRPC 患者。我们使用分子条形码对预处理 cfDNA 和配对的白细胞 DNA 进行了靶向测序，并使用内部管道检测了 VAF ≥0.1% 的 ctDNA 变体。我们研究了应用不同 ctDNA 分数截断值后的无进展生存期 (PFS) 和总生存期 (OS)。结果：对 100 名患者进行了分析（中位随访 10.7 个月）。即使在 ctDNA 分数低于 2% 的样本中，我们也检测到了有害的 ATM、BRCA2 和 TP53 变体。当应用 0.4% 的 ctDNA 分数截断值时，发现有和无 ATM 或 BRCA2 缺陷的患者的 PFS 和 OS 存在显着差异 [HR，2.52；95% 置信区间 (CI)，1.24–5.11；P = 0.0091] 和 TP53（HR，3.74；95% CI，1.60–8.71；P = 0.0014）。然而，当应用 2% 的 ctDNA 分数截断值时，不再观察到这些差异，并且大约 50% 的样本被归类为 ctDNA 不可量化。结论：用 VAF < 检测低频 ctDNA 变异