Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. Flowchart summarizing the experiments performed in this study and the sample numbers used at each step.
  • Fig. S2. Size distribution of cfDNA determined by sWGS for different cancer types.
  • Fig. S3. Insert size distribution of mutant cfDNA determined with hybrid-capture sequencing for 19 patients.
  • Fig. S4. DNA fragment size distribution for plasma samples from patients with ovarian cancer.
  • Fig. S5. Quality control assessed for in vitro size selection.
  • Fig. S6. Quality control assessed for in vitro and in silico size selection on healthy control samples.
  • Fig. S7. SCNA analysis of the segmental log2 ratio determined after sWGS (<0.4× coverage) for the patient OV04-83.
  • Fig. S8. SCNA analysis of the segmental log2 ratio determined after sWGS (<0.4× coverage) for plasma samples from patients with ovarian cancer (from the OV04 study).
  • Fig. S9. MAF and t-MAD score compared for different cancer types.
  • Fig. S10. t-MAD score measured on a plasma DNA dilution series.
  • Fig. S11. t-MAD scores and fragmentation features compared to tumor volume.
  • Fig. S12. Changes to t-MAD after in vitro size selection.
  • Fig. S13. SCNA analysis in cfDNA from plasma samples collected at baseline and after treatment for 13 patients with HGSOC.
  • Fig. S14. MAF for SNVs called by WES with and without size selection.
  • Fig. S15. TAm-Seq before and after in vitro size selection.
  • Fig. S16. Mutations in clinically relevant genes detected by WES with and without in silico size selection.
  • Fig. S17. Size distribution of nonmutant DNA and ctDNA concentration.
  • Fig. S18. ROC curve for individual fragmentation features in high ctDNA cancers versus controls.
  • Fig. S19. t-MAD score compared with seven fragmentation features.
  • Fig. S20. Performance metrics for the two algorithms, LR and RF.
  • Fig. S21. LR and RF models using the fragmentation features without t-MAD.
  • Legends for tables S1 to S6.
  • References (48, 49)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Summary table of the patients and samples included in this study.
  • Table S2 (Microsoft Excel format). Values for nine fragmentation features determined from sWGS data for the samples included in the study.
  • Table S3 (Microsoft Excel format). t-MAD score for the 48 plasma samples of the OV04 cohort before and after in vitro size selection.
  • Table S4 (Microsoft Excel format). Log2 of the signal ratio observed by sWGS of the plasma samples from the OV04 cohort.
  • Table S5 (Microsoft Excel format). Mutations called by WES of six patients selected from the OV04 cohort.
  • Table S6 (Microsoft Excel format). Mutations called by WES data of the plasma samples from 16 patients from the CoPPO cohort.