Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. Tumor mutation list characterization for INVAR.
  • Fig. S2. Use of patients and healthy individuals as controls in pooled sequencing panels.
  • Fig. S3. INVAR flowchart.
  • Fig. S4. Characterization of background error rates with bespoke error-suppression methods.
  • Fig. S5. Patient-specific outlier suppression.
  • Fig. S6. Background error rate per sample in personalized capture data.
  • Fig. S7. Signal weighting based on tumor allele fraction and fragment size, with consideration of intratumor heterogeneity.
  • Fig. S8. ctDNA dilution series with and without read collapsing.
  • Fig. S9. Comparison of input mass and IMAF observed and ROC curves for the stage IV melanoma cohort.
  • Fig. S10. Distribution of ctDNA fractions in plasma samples.
  • Fig. S11. Clinical correlates in advanced melanoma.
  • Fig. S12. Longitudinal tumor imaging and ctDNA data in advanced melanoma.
  • Fig. S13. Longitudinal individual plasma mutation data in advanced melanoma.
  • Fig. S14. Baseline characteristics and clinical correlates of ctDNA detection in early-stage melanoma.
  • Fig. S15. Background error rates and ROC curves in exome and sWGS data.
  • Fig. S16. Informative reads generated and hypothetical sensitivity with increased numbers of informative reads.
  • Legends for tables S1 to S6
  • References (5160)

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Other Supplementary Material for this manuscript includes the following:

  • Data file S1 contains the following tables:
  • Table S1 (Microsoft Excel format). Patient-specific mutation lists for melanoma cohorts.
  • Table S2 (Microsoft Excel format). Sample library preparation input, QC, and INVAR likelihood ratios—patient plasma samples.
  • Table S3 (Microsoft Excel format). Sample library preparation input, QC, and INVAR likelihood ratios—control plasma samples from healthy individuals.
  • Table S4 (Microsoft Excel format). Likelihood ratio thresholds and specificity values for each cohort.
  • Table S5 (Microsoft Excel format). Tumor volumes for the stage IV melanoma cohort.
  • Table S6 (Microsoft Excel format). Patient demographics for the melanoma cohorts.