Science Immunology

Supplementary Materials

The PDF file includes:

  • Materials
  • Fig. S1. Predictive power of neoantigen load.
  • Fig. S2. Predictive power of the neoantigen fitness model.
  • Fig. S3. Association of CSiN (A), neoantigen loads (B), and neoantigen fitness (C) with IL-2/SAbR treatment response in ccRCC patients.
  • Fig. S4. Prognostic power of neoantigen load.
  • Fig. S5. Prognostic power of the neoantigen fitness model.
  • Fig. S6. Association of CSiN, neoantigen loads, and neoantigen fitness with prognosis of patients with pediatric ALL and patients with LIHC.
  • Fig. S7. Cartoon showing the workflow of calculation of CSiN scores.
  • Fig. S8. The CSiN plot for the primary tumor of XP397 from the UTSW KCP cohort is shown.
  • Fig. S9. Validity of neoantigen predictions.
  • Fig. S10. The average number of neoantigens generated by each type of mutations.
  • Fig. S11. Demonstrating independence of CSiN from mutation load/neoantigen and transcriptomic-based biomarkers.
  • Fig. S12. Association of CSiN with metastasis.
  • Fig. S13. Validating the predictive power of CSiN, neoantigen load and neoantigen fitness model using OS/PFS as the criterion.
  • Fig. S14. Assessing the intra-tumor heterogeneity of CSiN and neoantigen loads.
  • Fig. S15. Calculating CSiN with only exome-seq data.
  • Fig. S16. Using the median + 2 x interquartile range cutoff on neoantigen load.
  • Fig. S17. Predictive value of class I-specific CSiN and class II-specific CSiN.
  • Fig. S18. Predictive value of class I-specific neoantigen fitness model measured by survival analyses (limiting to 9-mers from missense mutations).
  • Fig. S19. Predictive value of class I-specific neoantigen fitness model measured by categorical response variables (limiting to 9-mers from missense mutations).
  • Fig. S20. Predictive value of CSiN for the patients with high Teff signature expression.
  • Fig. S21. Predictive value of CSiN for the patients treated by sunitinib and by atezolizumab in the IMmotion150 cohort.
  • Fig. S22. Predictive value of CSiN for all the patients in the Hellmann cohort.
  • Fig. S23. Boxplots showing distribution of CSiN scores in quartiles of tumor clone number determined by pyclone.
  • Table S1. The patient cohorts used in this study.
  • Table S3. P values and false discovery rates of the tested cohorts shown in Figs. 2 and 3.

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Other Supplementary Material for this manuscript includes the following:

  • Table S2. Processed mutation, expression and neoantigen data of the IL-2 cohort (in Excel spreadsheet).
  • Data file S1. Raw data file for Figs. 1 to 3 (in Excel spreadsheet).

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