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bioRxiv · 10.1101/2025.08.22.671849

PRECOG update: An augmented resource of clinical outcome associations with gene expression for pediatric and immunotherapy cohorts

Benard, B. A.·Lalgudi, C. K.·Ilerten, I.·Wang, R.·Gentles, A. J.
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Abstract

Gene expression can be used to define prognostic and predictive biomarkers across cancers and treatment modalities. PRECOG (https://precog.stanford.edu) is a compendium of datasets with gene expression and clinical outcomes that facilitates visualization of associations between genomic profiles and patient survival. Here, we augment the existing PRECOG with new datasets in previously poorly represented adult cancer types, as well as adding annotated pediatric and immunotherapy treated cohorts. Pediatric PRECOG comprises [~]4,000 patients across 12 cancers; while the immunotherapy cohort (ICI PRECOG) contains [~]4,500 patients across 20 cancer subtypes from 80 distinct datasets across 52 studies. We compute and visualize associations of gene expression with survival outcomes using Cox regression for time-to-event, or logistic regression for responder vs non-responder, across all datasets. We also estimate cell type fractions in samples via computational deconvolution using CIBERSORTx, to identify survival associations at the level of cell types. All expression data, clinical annotations, and gene and cell type survival z-scores and meta z-scores for adult, pediatric, and ICI PRECOG, are available for interactive analysis and download, along with Kaplan-Meier and boxplot visualizations. This updated resource will provide new insights into biomarkers for specific therapies, populations, and cancer types. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/671849v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@13446bdorg.highwire.dtl.DTLVardef@11025fcorg.highwire.dtl.DTLVardef@12e017corg.highwire.dtl.DTLVardef@1637dba_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Benard, B. A., Lalgudi, C. K., Ilerten, I., Wang, R., Gentles, A. J.. 2025-08-28. PRECOG update: An augmented resource of clinical outcome associations with gene expression for pediatric and immunotherapy cohorts. https://doi.org/10.1101/2025.08.22.671849

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