Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. False-positive evaluation for somatic mutation callers.
  • Fig. S2. ddPCR mutation validation analyses.
  • Fig. S3. Precision-recall and ROC curve analyses of Cerebro and other mutation callers using experimentally validated alterations.
  • Fig. S4. Mutation loads of TCGA exomes using different mutation calling methods.
  • Fig. S5. Concordance rates (% of total mutations) of Cerebro compared to other mutation call sets for TCGA exomes.
  • Fig. S6. Response to checkpoint inhibitors associated with mutational load.
  • Fig. S7. Survival analysis by mutation load stratified by discovery and validation cohorts.
  • Fig. S8. Alterations confirmed by ddPCR in clinical NGS panel comparison.
  • Fig. S9. Comparative results of three clinical sequencing panels.

[Download PDF]

Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Confidence scoring model features for the Cerebro machine learning algorithm.
  • Table S2 (Microsoft Excel format). Performance results for simulated low-purity tumors.
  • Table S3 (Microsoft Excel format). False-positive rates of mutation calling methods.
  • Table S4 (Microsoft Excel format). Sensitivity results by variant type of mutation calling methods.
  • Table S5 (Microsoft Excel format). Sensitivity results for substitutions by MAF.
  • Table S6 (Microsoft Excel format). Sensitivity results for insertion-deletions by MAF.
  • Table S7 (Microsoft Excel format). Results of ddPCR validation of somatic mutations.
  • Table S8 (Microsoft Excel format). Performance results for cell lines with validated somatic mutations.
  • Table S9 (Microsoft Excel format). Unique and shared mutation load results for Cerebro and TCGA (MC3).
  • Table S10 (Microsoft Excel format). Concordance results for Cerebro and TCGA for driver oncogenes and tumor suppressor genes.
  • Table S11 (Microsoft Excel format). Comparison of mutation calls in immunotherapy publications and Cerebro reanalysis.
  • Table S12 (Microsoft Excel format). Evaluation of TruSeq false-positive calls using raw CS125 and Oncomine sequence data.
  • Table S13 (Microsoft Excel format). Comparison of mutation callers for clinical samples.
  • Table S14 (Microsoft Excel format). Shared and unique somatic mutation calls between Cerebro and TCGA.
  • Table S15 (Microsoft Excel format). Genomic ROIs used in clinical panel comparisons.