Fig. 2: Mutational landscape of HER2-negative primary breast cancers under neoadjuvant chemotherapy.

a Landscape of mutational alterations over time. Stacked plots display mutational burden (top), breast cancer drivers (tile plots, middle), PAM50 molecular intrinsic subtypes, clinical–pathological responses per patient and purity (tile plots, middle), mutation signatures (filled histogram). b Mutation clonality and subclonal distribution across different responses to eribulin. Left panels: odds for complete or partial response; right panels: a relative hazard for relapse-free survival (RFS). The analysis was performed for all comers (top panels) and for HR-positive and HR-negative patients (bottom panels). c Distribution of selected driver mutations generating neoantigens. Driver gene mutations are coloured whether the mutation is clonal or subclonal. d TILs across PAM50 intrinsic subtypes. (*) refer to p value < 0.05; ns nonsignificant. For each box plot, the centre line, the boundaries of the box, the ends of the whiskers and points beyond the whiskers represent the median value, the interquartile range, the minimum and maximum values, and the outliers, respectively. e Relationship between predicted neoantigen load (y-axis) and nonsynonymous mutational load (x-axis) and between predicted neoantigen load (y-axis) and mean stromal TILs per patient (x-axis).