120 Chapter 5 −2 −1 0 1 2 Stage IIIA carcinosarcoma Copy Number (log2 ratio) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 19 21 Tumor Fraction: 0.5545, Ploidy: 1.67 −2 −1 0 1 2 Stage IIIC serous carcinoma Copy Number (log2 ratio) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 19 21 Tumor Fraction: 0.09412, Ploidy: 1.67 −2 −1 0 1 2 Healthy control Copy Number (log2 ratio) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 19 21 Tumor Fraction: 0.04318, Ploidy: 1.92 A C B Figure 2: Copy number analysis in urine cell-free DNA. Illustrative examples of genome-wide somatic copy number profiles of urine supernatant samples collected from patients with a stage IIIA carcinosarcoma (A), stage IIIC serous carcinoma (B), and a healthy control (C). Estimated ploidy and tumor fraction are listed at the top of the plot. The y-axis depicts the log2 tumor to normal ratio. DISCUSSION Both elevated methylation levels of a subset of markers and SCNA were detected in home-collected urine samples of ovarian cancer patients by targeted qMSP assays and shallow whole-genome sequencing, respectively. Urine is truly non-invasive and unlocks at home collection of liquid biopsy to reduce in-person visits. Yet, an important finding was that methylation levels in benign cases were similarly high, presenting a challenge for the development of clinically useful tests. While we tested for methylation markers described and also by us verified to be associated with ovarian cancer, it was found that when tested in our patient-friendly sample types most of these did not distinguish benign from malignant ovarian
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