133 Molecular analysis for ovarian cancer detection in patient-friendly samples Table of contents Supplemental Figure 8 Genome-wide SCNA profiles of matched urine and FFPE primary tumor tissue The log2 tumor to normal ratio is depicted on the y-axis and the chromosomal position on the x-axis. Computed using ichorCNA software. FFPE = formalin-fixed paraffinembedded, SCNA = somatic copy number aberrations. Supplemental Figure 9 Scatter plot indicating the relation between MAL methylation levels and the tumor fraction as estimated by ichorCNA in urine supernatant samples. MAL methylation levels are shown by 2log-transformed Cq ratios. MAL was the most discriminating marker between urine supernatant samples of healthy controls and ovarian cancer patient and therefore plotted against the tumor fraction. The patient with the highest tumor fraction in urinary cfDNA also showed the highest MAL methylation, as seen in the upper right part of the plot. Cq = quantification cycle. Supplemental Figure 10 Fragment size distributions for cfDNA reads of urine supernatant samples from healthy controls (n=2) and ovarian cancer patients with a low (<5%, n=19) and high (≥5%, n=4) tumor fraction determined from shallow whole-genome sequencing. The cfDNA with a high tumor fraction revealed a shorter modal fragment size (80 bp) than cfDNA with a low tumor fraction and controls (111 bp). 5
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