Supplementary Materials

The PDF file includes:

  • Fig. S1. Fragment size distribution of cfDNA from individual healthy plasma samples.
  • Fig. S2. Fragment size distribution of cfDNA from individual healthy urine samples.
  • Fig. S3. Comparison of raw sequencing coverage between plasma and urine.
  • Fig. S4. Distribution of RPR widths across multiple genome-wide RPR maps.
  • Fig. S5. Comparison of overlapping and nonoverlapping RPR call confidence scores.
  • Fig. S6. Comparison of fragment size in urine cfDNA between open and closed chromatin regions, using bins of 50, 500, and 1000 kb.
  • Fig. S7. Cosine similarity between cfDNA fragment sizes and DHS sites.
  • Fig. S8. Mean pooled plasma and urine cfDNA sequencing depth at the TSS of genes grouped according to their expression.
  • Fig. S9. Spearman’s rank correlation coefficients for cfDNA sequencing coverage at NDR coverage and gene expression.
  • Fig. S10. Changes in rank based on the correlation between NDR coverage and gene expression between plasma and urine.
  • Fig. S11. Nucleotide frequencies at fragment start sites in plasma samples.
  • Fig. S12. Nucleotide frequencies at fragment end sites in plasma samples.
  • Fig. S13. Nucleotide frequencies at fragment start sites in urine samples.
  • Fig. S14. Nucleotide frequencies at fragment end sites in urine samples.
  • Fig. S15. Nucleotide frequencies at fragment start and end sites across fragment size bins in plasma and urine cfDNA.
  • Fig. S16. Fragment size distribution in individual urine samples from patients with cancer.
  • Fig. S17. Effect of changing maximum distance from RPR center on fraction of fragments with ends within RPRs in urine samples from healthy controls and patients with cancer.
  • Fig. S18. Nucleotide frequencies at fragment start sites in urine samples from patients with cancer.
  • Fig. S19. Nucleotide frequencies at fragment end sites in urine samples from patients with cancer.
  • Fig. S20. ROC analysis for classifying control and cancer samples by cancer type.
  • Fig. S21. Aberrant fragments across copy number changes in sample 36.
  • Fig. S22. Aberrant fragments across copy number changes in sample 37.
  • Fig. S23. Aberrant fragments across copy number changes in sample 34.
  • Fig. S24. Aberrant fragments across copy number changes in sample 43.
  • Fig. S25. Aberrant fragments across copy number changes in sample 33.
  • Fig. S26. Comparison of fragment size distributions between multiple urine samples collected from five healthy individuals.
  • Table S1. Histone proteins identified in urine using mass spectrometry.
  • Table S2. Clinical characteristics of patients with cancer.
  • Legends for data files S1 to S4

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Other Supplementary Material for this manuscript includes the following:

  • Data file S1 (Microsoft Excel format). Quantile normalized cosine similarity between DHS sites and cfDNA fragment size.
  • Data file S2 (Microsoft Excel format). Quantile normalized Spearman’s rank correlation coefficients between gene expression and NDR coverage.
  • Data file S3 (Microsoft Excel format). Rank changes in Spearman’s rank correlation coefficients across pooled plasma and urine.
  • Data file S4 (Microsoft Excel format). FAF and multidimensional scaled dimensions 1 to 4 of FEMs in urine samples.