Comparative analysis of regression algorithms for drug response prediction using GDSC dataset

• Published in: BMC research notes Vol. 18; no. Suppl 1; pp. 10 - 9
• Main Authors: Ha, Soojung, Park, Juho, Jo, Kyuri
• Format: Journal Article
• Language: English
• Published: London BioMed Central 13.01.2025; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Accuracy; Algorithms; Bioinformatics; Biomedical and Life Sciences; Biomedicine; Cancer; Comparative analysis; Computational Biology - methods; Copy number; Datasets; Drug response; Drug therapy; Feature selection; GDSC dataset; Gene expression; Genomics; Genomics - methods; Humans; Life Sciences; Machine learning; Medicine/Public Health; Multiomics; Neoplasms - drug therapy; Neoplasms - genetics; Next-generation sequencing; Pharmacology, Experimental; Physiological aspects; Prediction models; Python; Regression; Regression Analysis; Researchers; Support Vector Machine; South Korea; Regression; Drug response; Multiomics; Gene expression; GDSC dataset
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-024-07026-w

Background Drug response prediction can infer the relationship between an individual’s genetic profile and a drug, which can be used to determine the choice of treatment for an individual patient. Prediction of drug response is recently being performed using machine learning technology. However, high-throughput sequencing data produces thousands of features per patient. In addition, it is difficult for researchers to know which algorithm is appropriate for prediction as various regression and feature selection algorithms exist. Methods We compared and evaluated the performance of 13 representative regression algorithms using Genomics of Drug Sensitivity in Cancer (GDSC) dataset. Three analyses was conducted to show the effect of feature selection methods, multiomics information, and drug categories on drug response prediction. Results In the experiments, Support Vector Regression algorithm and gene features selected with LINC L1000 dataset showed the best performance in terms of accuracy and execution time. However, integration of mutation and copy number variation information did not contribute to the prediction. Among the drug groups, responses of drugs related with hormone-related pathway were predicted with relatively high accuracy. Conclusion This study can help bioinformatics researchers design data processing steps and select algorithms for drug response prediction, and develop a new drug response prediction model based on the GDSC or other high-throughput sequencing datasets.