Fig. 1: Study design, workflow, and analytical validity. | Nature Communications

Fig. 1: Study design, workflow, and analytical validity.

From: The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer

Fig. 1

a A retrospective cohort of 1,082 formalin-fixed paraffin-embedded (FFPE) breast cancer samples underwent multiplexed RNA-FISH-guided laser capture microdissection (LCM) coupled with RNA-sequencing. Annotation of the tumor on a hematoxylin and eosin (H&E) section and the biomarker expression derived from multiplexed RNA-FISH were used to select regions of interest (ROIs) for LCM from cresyl violet sections. These tumor-enriched samples were then sequenced to characterize gene expression signatures to provide diagnostic, prognostic, and predictive inferences from the cohort clinical data. DEGs, Differential expressed genes; IHC, immunohistochemistry. Created with BioRender.com. b Analytical validity of mFISHseq compared to immunohistochemistry assessed by receiver operating characteristic (ROC) curves in 1013 breast tumors stratified into 70:30 training (n = 701) and test (n = 312) datasets. AUC, area under the curve. The table shows biomarker thresholds defined in the training set by maximizing concordance (Cohen’s κ) between RNA-SEQ transcripts per million (TPM) expression values and immunohistochemistry results for each biomarker. These thresholds were then applied to the test set. Source data are provided as a Source Data file.

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