Value of genomics- and radiomics-based machine learning models in the identification of breast cancer molecular subtypes: a systematic review and meta-analysis

BACKGROUND: In the era of precision therapy, early classification of breast cancer (BRCA) molecular subtypes has clinical significance for disease management and prognosis. We explored the accuracy of machine learning (ML) models for early classification of BRCA molecular subtypes through a systematic review of the literature currently available. METHODS: We retrieved relevant studies published in PubMed, EMBASE, Cochrane, and Web of Science until 15 April 2022. A prediction model risk of bias assessment tool (PROBAST) was applied for the assessment of risk of bias of a genomics-based ML model, and the Radiomics Quality Score (RQS) was simultaneously used to evaluate the quality of this radiomics-based ML model. A random effects model was adopted to analyze the predictive accuracy of genomics-based ML and radiomics-based ML for Luminal A, Luminal B, Basal-like or triple-negative breast cancer (TNBC), and human epidermal growth factor receptor 2 (HER2). The PROSPERO of our study was prospectively registered (CRD42022333611). RESULTS: Of the 38 studies were selected for analysis, 14 ML models were based on gene-transcriptomic, with only 4 external validations; and 43 ML models were based on radiomics, with only 14 external validations. Meta-analysis results showed that c-statistic values of the ML based on radiomics for the identification of BRCA molecular subtypes Luminal A, Luminal B, Basal-like or TNBC, and HER2 were 0.76 [95% confidence interval (CI): 0.60–0.96], 0.78 (95% CI: 0.69–0.87), 0.89 (95% CI: 0.83–0.91), and 0.83 (95% CI: 0.81–0.86), respectively. The c-statistic values of ML based on the gene-transcriptomic analysis cohort for the identification of the previously described BRCA molecular subtypes were 0.96 (95% CI: 0.93–0.99), 0.96 (95% CI: 0.93–0.99), 0.98 (95% CI: 0.95–1.00), and 0.97 (95% CI: 0.96–0.98) respectively. Additionally, the sensitivity of the ML model based on radiomics for each molecular subtype ranged from 0.79 to 0.85, while the sensitivity of the ML model based on gene-transcriptomic was between 0.92 and 0.99. CONCLUSIONS: Both radiomics and gene transcriptomics produced ideal effects on BRCA molecular subtype prediction. Compared with radiomics, gene transcriptomics yielded better prediction results, but radiomics was simpler and more convenient from a clinical point of view.