Multiomic integration reveals subtype-specific predictors of neoadjuvant treatment response in breast cancer.

In the Hurvitz2020 cohort ( 48 ), the expression difference approached significance ( P = 0.059) in the treatment regimen with the largest sample size (fig.

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Initially, we examined the distribution of gene expression through t-distributed stochastic neighbor embedding (t-SNE) and found that samples belonging to the same subtype showed a trend to cluster together ( Fig. 4A ).

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When comparing methylation levels between pCR and RD groups within each subtype, we identified elevated methylation in the distal enhancer-like signature region ( P = 0.076) and the CCCTC-Binding Factor (CTCF)-only region ( P = 0.060) in the ER + HER2 + subtype, although these differences did not reach statistical significance ( Fig. 3A ).

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