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Fig. 2 | Breast Cancer Research

Fig. 2

From: On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer

Fig. 2

Responders and non-responders are more distinct on than before treatment. a Supervised clustering using local Fisher discriminant analysis (LFDA) indicates that as early as 2 weeks on treatment, there is a visible separation of the response classes that were unseen in the pre-treatment samples in the NEO dataset. Red = non-responder, orange = partial responder, blue = complete responder. b Greater numbers of genes are under and overexpressed between responders and non-responders on treatment. The three lines represent different statistical thresholds (*p < 0.05, **p < 0.01, and ***p < 0.001 or FDR = 10%, FDR = 5%, and FDR = 1%, gene lists are in Additional file 4: Tables S2 and S3) in the NEO dataset. c Sankey diagram illustrating the proportions of tumours that change or maintain PAM50 intrinsic subtype during chemotherapy treatment. Whilst basal subtypes remain mostly stable, the composition of the cohort changes with treatment time, which may help to identify responsive or non-responsive patients. PT = pre-treatment, T-ON = on-treatment

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