Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers.

To test the efficacy of the score, we first identified TCGA breast cancer patients with high infiltrating lymphocyte levels based on evaluation of tumor slides by trained histopathologists and found patients with high lymphocytes levels show significantly higher CTL scores than those with low lymphocyte infiltration ( P = 3.86 × 10 −5 ), though CTLs as evaluated by CIBERSORT failed to reach statistical significance when performing the same analysis ( P = 0.11) (Supplementary Fig. 3A ).

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