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bioRxiv · 10.1101/2025.02.27.640548

Identification of Multiple Prognostic Biomarker Sets for Risk Stratification in SKCM

Malik, S.·Tomer, R.·Arora, A.·Raghava, G. P. S.
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Abstract

Most of the existing studies have identified a single profile of prognostic biomarkers for predicting high-risk cancer patients using transcriptomics data. In this study, we propose multiple distinct sets of prognostic biomarkers for predicting high-risk Skin Cutaneous Melanoma (SKCM) patients. Our primary analysis reveals that the expression of certain genes, such as CREG1, PCGF5, and VPS13C, strongly correlates with overall survival (OS) in SKCM patients. We developed machine learning-based prognostic models to predict 1-, 3-, and 5-year overall survival using gene expression profiles. State-of-the-art feature selection techniques were employed to identify the first prognostic biomarkers set consisting of 20 genes. Machine learning models built to predict high-risk patients using this set of biomarkers and achieved an AUC of 0.90 and a Kappa of 0.58 in distinguishing high-risk SKCM patients. Similarly, a second independent set of 20 prognostic genes was identified, with no overlap with the first set. The best model trained on this second set achieved an AUC of 0.89 with a Kappa of 0.56, while the fifth biomarker set achieved the highest performance with an AUC of 0.91 and a Kappa of 0.64. This process was repeated to obtain a total of seven distinct prognostic biomarker sets, each containing 20 unique genes. The predictive performance of these models varied between 0.84 and 0.91 for AUC and 0.48 to 0.64 for Kappa on the validation dataset. These findings demonstrate that it is possible to identify multiple independent sets of prognostic biomarkers, each capable of accurately predicting high-risk SKCM patients. HighlightsO_LIPrediction of high-risk SKCM patients from transcriptomics data C_LIO_LIIdentification of multiple set of prognostic biomarkers C_LIO_LIIdentification of set of biomarkers using feature selection technique C_LIO_LIDevelopment of machine learning based models for prediction C_LIO_LIPathway analysis of selected set of biomarker genes C_LI

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Malik, S., Tomer, R., Arora, A., Raghava, G. P. S.. 2025-03-05. Identification of Multiple Prognostic Biomarker Sets for Risk Stratification in SKCM. https://doi.org/10.1101/2025.02.27.640548

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