FIG 2.

Validation of total tumor-infiltrating lymphocyte (TIL) gene signature scores. (A) For a subset of basal-like patients from The Cancer Genome Atlas (TCGA) with previously published histologic TIL scores (n = 156) according to Danaher et al,¹⁹ the total TIL gene signature scores (x-axis) were correlated with histologic stromal TIL counts (y-axis). The 75th percentile of histologic (35% stromal TILs) and gene signature TIL scores (5.92) are represented by dashed black lines. Tumor subtype is reflected by point color (estrogen receptor–positive breast cancers [ER-positive BCs], n = 21; triple-negative BCs ([TNBCs], n = 135). The linear regression line with 95% CIs is shown in blue. Pearson’s R = 0.44; P = 1.18E-08. (B-D) For all patients with ER-positive BCs (n = 697) and TNBCs (n = 191) in TCGA, patients were classified as immune cell “High” (Danaher et l¹⁹ total TIL gene signature score in the top 25th percentile) or “Low” (Danaher total TIL gene signature scores in the bottom 75th percentile), represented on the x-axis. Distributions of (B) PAM50 subtypes, (C) Ki-67 expression categories and (D) tumor mutation burden (TMB) categories were compared between patients with immune-rich high and low ER-positive BCs and TNBCs separately. PAM50 and TMB categories were obtained from previous publications, and Ki-67 categories were defined as greater than (high) or less than (low) the median Ki-67 expression level across all patients.