A liquid biopsy is a test that evaluates the status of a disease by analyzing a sample of bodily fluid, most commonly blood. In recent years, there has been progress in the development and clinical application of liquid biopsy methods to identify blood-based, tumor-specific biomarkers for many cancer types. However, the implementation of these technologies to aid in the treatment of patients who have a sarcoma remains behind other fields of cancer medicine. For this study, we chose to evaluate a sarcoma liquid biopsy based on circulating tumor DNA (ctDNA). All human beings have normal cell-free DNA (cfDNA) circulating in the blood. In contrast with cfDNA, ctDNA is genetic material present in the blood stream that is derived from a tumor. ctDNA carries the unique genomic fingerprint of the tumor with changes that are not present in normal circulating cfDNA. A successful ctDNA liquid biopsy must be able to target these tumor-specific genetic alterations. For instance, epidermal growth factor receptor (EGFR) mutations are common in lung cancers, and ctDNA liquid biopsies are currently in clinical use to evaluate the status of disease in patients who have a lung cancer by detecting EGFR mutations in the blood. As opposed to many carcinomas, sarcomas do not have common recurrent mutations that could serve as the foundation to a ctDNA liquid biopsy. However, many sarcomas have structural changes to their chromosomes, including gains and losses of portions or entire chromosomes, known as copy number alterations (CNAs), that could serve as a target for a ctDNA liquid biopsy. Murine double minute 2 (MDM2) amplification in select lipomatous tumors or parosteal osteosarcoma is an example of a CNA due to the presence of extra copies of a segment of the long arm of chromosome 12. Since a majority of sarcomas demonstrate a complex karyotype with numerous CNAs, a blood-based liquid biopsy strategy that searches for these CNAs may be able to detect the presence of sarcoma ctDNA. Whole-genome sequencing (WGS) is a next-generation sequencing technique that evaluates the entire genome. The depth of coverage of WGS refers to how detailed the sequencing is, like higher versus lower power on a microscope. WGS can be performed with high-depth sequencing (that is, > 60×), which can detect individual point mutations, or low-depth sequencing (that is, 0.1× to 5×), referred to as low-passage whole-genome sequencing (LP-WGS), which may not detect individual mutations but can detect structural chromosomal changes including gains and losses (that is, CNAs). While similar strategies have shown favorable early results for specific sarcoma subtypes, LP-WGS has not been evaluated for applicability to the broader population of patients who have a sarcoma.

中文翻译：

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液体活检能否通过低传代全基因组测序检测肉瘤患者的循环肿瘤 DNA？试点评估。


液体活检是一种通过分析体液样本（最常见的是血液）来评估疾病状态的测试。近年来，液体活检方法的开发和临床应用取得了进展，以识别多种癌症类型的血液肿瘤特异性生物标志物。然而，这些技术在帮助治疗肉瘤患者方面的实施仍然落后于癌症医学的其他领域。在本研究中，我们选择评估基于循环肿瘤 DNA (ctDNA) 的肉瘤液体活检。所有人类的血液中都有正常的游离 DNA (cfDNA) 循环。与 cfDNA 相比，ctDNA 是存在于源自肿瘤的血流中的遗传物质。 ctDNA 携带肿瘤独特的基因组指纹，具有正常循环 cfDNA 中不存在的变化。成功的 ctDNA 液体活检必须能够针对这些肿瘤特异性基因改变。例如，表皮生长因子受体（EGFR）突变在肺癌中很常见，ctDNA液体活检目前在临床上用于通过检测血液中的EGFR突变来评估肺癌患者的疾病状态。与许多癌症不同，肉瘤不具有可作为 ctDNA 液体活检基础的常见复发突变。然而，许多肉瘤的染色体发生结构变化，包括部分或整个染色体的增加和丢失，称为拷贝数改变 (CNA)，这可以作为 ctDNA 液体活检的目标。由于 12 号染色体长臂片段存在额外拷贝，特定脂肪瘤或骨旁骨肉瘤中的鼠双微体 2 (MDM2) 扩增就是 CNA 的一个例子。 由于大多数肉瘤表现出具有大量 CNA 的复杂核型，因此搜索这些 CNA 的基于血液的液体活检策略可能能够检测肉瘤 ctDNA 的存在。全基因组测序（WGS）是评估整个基因组的下一代测序技术。 WGS 的覆盖深度是指测序的详细程度，例如显微镜上的高倍率与低倍率。 WGS可以进行高深度测序（即> 60×），可以检测单个点突变，也可以进行低深度测序（即0.1×至5×），称为低传代全基因组测序 (LP-WGS)，可能无法检测个体突变，但可以检测染色体结构变化，包括获得和丢失（即 CNA）。虽然类似的策略已显示出对特定肉瘤亚型有利的早期结果，但尚未评估 LP-WGS 对于更广泛的肉瘤患者群体的适用性。