Department of Pathology, Stanford University School of Medicine, Stanford, California.
Cancer Cytopathol. 2020 Jan;128(1):43-56. doi: 10.1002/cncy.22205. Epub 2019 Nov 21.
Liquid biopsy using cell-free DNA (cfDNA) presents new opportunities for solid tumor genotyping. While studies have demonstrated the utility of cfDNA from plasma, cfDNA from other body fluids remains underexplored.
We evaluated the molecular features and clinicopathologic correlates of cfDNA from serous body cavity fluids by performing hybrid capture-based next-generation sequencing (NGS) on cfDNA isolated from residual effusion supernatants. Twenty-one serous effusions from pleural (n = 15), peritoneal (n = 5), and pericardial (n = 1) cavity were analyzed.
The supernatants provided a median cfDNA concentration of 10.3 ng/µL. Notably, all effusions were sequenced successfully to a median depth >1000×, revealing a broad range of genetic alterations including single nucleotide variants, small insertions and deletions, amplifications, and fusions. Specifically, pathogenic alterations were identified in all malignant fluids (13/13), all fluids suspicious for malignancy (2/2), and 1 benign fluid (1/6) from a patient with metastatic cancer. To validate our findings, we examined matching results from 11 patients who underwent additional testing using formalin-fixed, paraffin-embedded (FFPE) specimens. In 8 patients, the paired results between FFPE and supernatant testing were concordant, whereas in the remaining 3 patients, supernatant analysis identified additional variants likely associated with resistance to targeted therapies. Additional comparison between FFPE and supernatant testing showed no difference in DNA concentration (P = .5), depth of coverage (P = .6), or allele frequency of pathogenic mutations (P = .7).
cfDNA isolated from serous body cavity fluids represents a promising source of genomic input for targeted NGS.
利用游离 DNA（cfDNA）进行液体活检为实体瘤基因分型带来了新的机遇。虽然已有研究证实了血浆 cfDNA 的应用价值，但其他体液来源的 cfDNA 仍有待进一步探索。
我们通过对从胸腔积液、腹腔积液和心包积液等体腔残留上清液中提取的 cfDNA 进行基于杂交捕获的下一代测序（NGS），评估了体腔液 cfDNA 的分子特征及其与临床病理的相关性。共分析了 21 例来自胸腔（n=15）、腹腔（n=5）和心包（n=1）腔的浆液性积液。
上清液中 cfDNA 的平均浓度为 10.3ng/µL。值得注意的是，所有积液均成功测序至平均深度>1000×，揭示了广泛的遗传改变，包括单核苷酸变异、小插入和缺失、扩增和融合。具体而言，所有恶性积液（13/13）、所有疑似恶性的积液（2/2）和 1 例转移性癌症患者的良性积液（1/6）中均发现了致病性改变。为了验证我们的发现，我们对 11 例额外采用福尔马林固定、石蜡包埋（FFPE）标本进行检测的患者的匹配结果进行了检测。在 8 例患者中，FFPE 和上清液检测的配对结果一致，而在其余 3 例患者中，上清液分析鉴定了可能与靶向治疗耐药相关的额外变异。FFPE 和上清液检测之间的进一步比较显示，DNA 浓度（P=0.5）、覆盖深度（P=0.6）或致病性突变等位基因频率（P=0.7）均无差异。
从浆液性体腔液中分离的 cfDNA 是靶向 NGS 的有前途的基因组输入源。
