119 Molecular analysis for ovarian cancer detection in patient-friendly samples between paired samples to assess their correlation (Supplemental Figure 7). Paired cervical scrapes and urine were available for 23 ovarian cancer patients. Individual markers in full void urine correlated moderately to strongly with urine supernatant (r = 0.52-0.61) and urine sediment (r = 0.67-0.76). The full void urine showed the best correlation with cervical scrapes (r = 0.42-0.59), while a weak correlation was observed between the urine supernatant and cervical scrapes (r = 0.33-0.45). Copy number aberrations are detectable in urine cell-free DNA The presence of ovarian cancer-derived DNA in the urine was verified by analyzing a subset of 25 urine supernatant samples of ovarian cancer patients (n=23) and healthy controls (n=2) by shallow whole-genome sequencing. Sequencing yielded a sufficient read count for all samples (median mapped paired read count of 55,133,492). Shallow whole-genome sequencing coverage and quality statistics per urine sample are provided in Supplemental Table 3. Aberrant genome-wide copy number profiles were found in 4 out of 23 sequenced urine supernatant samples of ovarian cancer patients (Figure 2, Supplemental Figure 8). Copy number profile concordance between urine and the primary tumor tissue was verified for these cases (Supplementary Figure 8). The patient with the highest tumor fraction also showed the highest methylation levels of MAL in the urine supernatant (Supplemental Figure 9). Additionally, fragment size distributions were analyzed by comparing cfDNA reads of healthy controls and ovarian cancer patients with low and high tumor fractions. Cancer samples with a high tumor fraction (n=4) revealed a shorter modal fragment size of 80 bp as compared to 111 bp in cancer samples with a low tumor fraction (n=19) and controls (n=2; Supplemental Figure 10). 5
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