To evaluate whether low coverage whole genome sequencing is suitable for the detection of malignant pelvic mass and compare its diagnostic value with traditional tumor markers. We enrolled 63 patients with a pelvic mass suspicious for ovarian malignancy. Each patient underwent low coverage whole genome sequencing (LCWGS) and traditional tumor markers test. The pelvic masses were finally confirmed via pathological examination. The copy number variants (CNVs) of whole genome were detected and the Stouffers Z-scores for each CNV was extracted. The risk of malignancy (RM) of each suspicious sample was calculated based on the CNV counts and Z-scores, which was subsequently compared with ovarian cancer markers CA125 and HE4, and the risk of ovarian malignancy algorithm (ROMA). Receiver Operating Characteristic Curve (ROC) were used to access the diagnostic value of variables. As confirmed by pathological diagnosis, 44 (70%) patients with malignancy and 19 patients with benign mass were identified. Our results showed that CA125 and HE4, the CNV, the mean of Z-scores (Zmean), the max of Z-scores (Zmax), the RM and the ROMA were significantly different between patients with malignant and benign masses. The area under curve (AUC) of CA125, HE4, CNV, Zmax, and Zmean was 0.775, 0.866, 0.786, 0.685 and 0.725 respectively. ROMA and RM showed similar AUC (0.876 and 0.837), but differed in sensitivity and specificity. In the validation cohort, the AUC of RM was higher than traditional serum markers. In conclusion, we develop a LCWGS based method for the identification of pelvic mass of suspicious ovarian cancer. LCWGS shows accurate result and could be complementary with the existing diagnostic methods.

中文翻译：

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应用低覆盖度全基因组测序检测恶性卵巢肿块

评估低覆盖度全基因组测序是否适用于盆腔恶性肿块的检测，并与传统肿瘤标志物比较其诊断价值。我们招募了 63 名疑似卵巢恶性肿瘤的盆腔肿块患者。每名患者都接受了低覆盖度全基因组测序（LCWGS）和传统的肿瘤标志物检测。最后经病理检查证实为盆腔肿块。检测全基因组的拷贝数变异 (CNV) 并提取每个 CNV 的 Stouffers Z 分数。根据 CNV 计数和 Z 值计算每个可疑样本的恶性风险 (RM)，随后将其与卵巢癌标志物 CA125 和 HE4 以及卵巢恶性风险算法 (ROMA) 进行比较。接收者操作特征曲线 (ROC) 用于访问变量的诊断值。经病理诊断证实，44例（70%）为恶性肿瘤，19例为良性肿块。我们的结果表明，CA125和HE4、CNV、Z分数的平均值（Zmean）、Z分数的最大值（Zmax）、RM和ROMA在恶性和良性肿块患者之间存在显着差异。CA125、HE4、CNV、Zmax 和 Zmean 的曲线下面积 (AUC) 分别为 0.775、0.866、0.786、0.685 和 0.725。ROMA 和 RM 显示出相似的 AUC（0.876 和 0.837），但敏感性和特异性不同。在验证队列中，RM 的 AUC 高于传统的血清标志物。总之，我们开发了一种基于 LCWGS 的方法，用于识别可疑卵巢癌的盆腔肿块。