Deep learning approaches for resolving genomic discrepancies in cancer: a systematic review and clinical perspective

Discrepancies in cancer sequencing data continue to pose significant challenges for accurate mutation detection, potentially resulting in misdiagnoses and suboptimal treatment strategies. Although deep learning (DL) has emerged as a transformative approach for identifying and rectifying these errors, there remains a lack of comprehensive evaluation of DL architectures, performance benchmarks, and clinical translation. In this systematic review of 78 studies (2015-2024), We synthesize recent advancements in DL methodologies for identifying genomic discrepancies, demonstrating that convolutional and graph-based architectures currently achieve state-of-the-art performance in variant calling and tumor stratification. DL models reduce false-negative rates by 30%-40% compared to traditional pipelines, with methods such as MAGPIE prioritizing pathogenic variants with 92% accuracy. However, challenges such as data scarcity, batch effects, and the interpretability of "black-box" models persist. We propose a future research roadmap advocating federated learning to enhance data privacy and attention mechanisms to improve model transparency. By bridging bioinformatics and oncology, this review offers actionable insights to expedite the deployment of DL in precision cancer therapy.