Table_3_Whole-genome/exome analysis of circulating tumor DNA and comparison to tumor genomics from patients with heavily pre-treated ovarian cancer: subset analysis of the PERMED-01 trial.xlsx

IntroductionThe poor prognosis of ovarian carcinoma (OvC) is due to the advanced stage at diagnosis, a high risk of relapse after first-line therapies, and the lack of efficient treatments in the recurrence setting. Circulating tumor DNA (ctDNA) analysis is a promising tool to assess treatment-resistant OvC and may avoid iterative tissue biopsies. We aimed to evaluate the genomic profile of recurrent heavily pre-treated OvC.
MethodsWe performed tumor panel-based sequencing as well as low-coverage whole-genome sequencing (LC-WGS) of tumor and plasma collected in patients with ovarian cancer included in the PERMED-01 trial. Whole-exome sequencing (WES) data of plasma samples were also analyzed and compared to mutation and copy number alteration (CNA) tumor profiles. The prognostic value [progression-free survival (PFS)] of these alterations was assessed in an exploratory analysis.
ResultsTumor and plasma genomic analyses were done for 24 patients with heavily pretreated OvC [67% high-grade serous carcinoma (HGSC)]. Tumor mutation burden was low (median 2.04 mutations/Mb) and the most frequent mutated gene was TP53 (94% of HGSC). Tumor CNAs were frequent with a median of 50% of genome altered fraction. Plasma LC-WGS and WES detected ctDNA in 21/24 cases (88%) with a median tumor fraction of 12.7%. We observed a low correlation between plasma and tumor CNA profiles. However, this correlation was significant in cases with the highest circulating tumor fraction. Plasma genome altered fraction and plasma mutation burden (p = 0.011 and p = 0.041, respectively, log-rank tests) were associated with PFS.
ConclusionsCombination of LC-WGS and WES can detect ctDNA in most pre-treated OvCs. Some ctDNA characteristics, such as genome altered fraction and plasma mutation burden, showed prognostic value. ctDNA assessment with LC-WGS may be a promising and non-expansive tool to evaluate disease evolution in this disease with high genomic instability.
Clinical Trial Registrationhttps://clinicaltrials.gov/ct2/show/NCT02342158, identifier NCT02342158.

**引言** 卵巢癌（ovarian carcinoma, OvC）预后不佳的原因在于确诊时多已处于晚期、一线治疗后复发风险高，且复发阶段缺乏有效的治疗手段。循环肿瘤DNA（circulating tumor DNA, ctDNA）分析是评估治疗耐药性卵巢癌的极具前景的工具，还可避免反复进行组织活检。本研究旨在评估经多线治疗的复发性卵巢癌的基因组特征。
**方法** 本研究对PERMED-01临床试验纳入的卵巢癌患者的肿瘤组织及血浆样本，分别开展基于肿瘤基因panel的测序以及低覆盖度全基因组测序（low-coverage whole-genome sequencing, LC-WGS）。同时对血浆样本的全外显子测序（whole-exome sequencing, WES）数据进行分析，并与肿瘤的突变及拷贝数变异（copy number alteration, CNA）特征进行对比。本研究还通过探索性分析评估了上述变异的预后价值[无进展生存期（progression-free survival, PFS）]。
**结果** 本研究对24名经多线治疗的复发性卵巢癌患者开展了肿瘤组织与血浆的基因组分析，其中67%为高级别浆液性癌（high-grade serous carcinoma, HGSC）。肿瘤突变负荷较低，中位值为2.04突变/Mb；最常见的突变基因为TP53，在HGSC患者中占比达94%。肿瘤拷贝数变异频发，基因组改变分数的中位值为50%。通过血浆LC-WGS与WES检测，21/24例（88%）样本中检出ctDNA，其肿瘤分数的中位值为12.7%。本研究观察到血浆与肿瘤的CNA特征相关性较低，但在循环肿瘤分数最高的病例中，该相关性具有统计学意义。血浆基因组改变分数与血浆突变负荷分别经log-rank检验后p值为0.011与0.041，二者均与PFS显著相关。
**结论** 联合应用LC-WGS与WES可在多数经多线治疗的卵巢癌患者中检出ctDNA。部分ctDNA特征（如基因组改变分数与血浆突变负荷）具有预后价值。对于这类基因组高度不稳定的疾病，采用LC-WGS进行ctDNA检测或许是一种极具前景且无创的工具。
**临床试验注册** https://clinicaltrials.gov/ct2/show/NCT02342158，识别编号为NCT02342158。