Fig. 2

Mutational burden, potential neoepitopes, and expressed neoepitopes in breast cancer determined using Epitopehunter. (a) The mutational load is highest in triple negative breast cancer (TNBC), followed by the HER-2(+) breast cancer subtype, and least for the ER/PR(+)HER-2(−) subtype. The median and range of non-synoymous mutations per cancer type are: 32 (1–2860) in ER/PR(+)HER-2(−), 39 (1–1206) in HER-2(+) and 63 (2–765) in TNBC. The number of samples in each subtype are: 630 (ER/PR(+)HER-2(−)), 141 (HER-2(+)), 99 (TNBC). (b) The range of potential binding neoepitopes (IEDB score ≤ 500 nM) is highest for the TNBC subtype, followed by HER-2(+); and lowest for the ER/PR(+)HER-2(−) subtype. The median and range of high affinity binding neoepitopes are as follows: 10 (0–864) in ER/PR(+)HER-2(−), 15 (0–717) in HER-2(+) and 26 (0–237) in TNBC. The number of samples in each subtype are: 586 (ER/PR(+)HER-2(−)), 138 (HER-2(+)), 93 (TNBC). (c) The median and range of predicted neoepitope with expression (FPKM ≥5) across breast cancer subtypes are: 3 (0–230) in ER/PR(+)HER-2(−), 4 (0–226) in HER-2(+) and 8(0–82) in TNBC. The number of samples in each case are: 583(ER/PR(+)HER-2(−)), 138(HER-2(+)), 92(TNBC). Significant differences between subtypes of cancer are computed pairwise for each breast cancer subtype using a Wilcox rank sum test, *** P < 0.001 ** P < 0.01