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Next-generation sequencing in breast cancer: current clinical applications and future directions.

Nur Fatihah Mohd Zuhdi·Alaa Siddig·Siti Norasikin Mohd Nafi·Md Salzihan Md Salleh·Maya Mazuwin Yahya·Wan Zainira Wan Zain·Tengku Ahmad Damitri Al-Astani Tengku Din·Wan Faiziah Wan Abdul Rahman
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Abstract

INTRODUCTION: Breast cancer is a heterogeneous disease that claims 670,000 lives by 2022. Omic technologies, particularly next generation sequencing (NGS) offers promising avenues for precision medicine. American Society of Clinical Oncology (ASCO) outlines genomic testing's utility, emphasizing prognostic and diagnostic potential. OBJECTIVES: This review succinctly explores NGS's evolution and clinical applications of NGS in breast cancer, thereby guiding future research to enhance patient care. METHODS: Comprehensive literature searches were conducted using databases such as PubMed, Google Scholar, and ResearchGate, focusing on keywords including breast cancer, HER-2 low breast cancer, circulating tumour DNA, single-cell RNA sequencing, and next-generation sequencing. Peer-reviewed, high-quality articles published in English were selected for inclusion. RESULTS: Previous studies have explored the evolution of NGS technology and its clinical applications in breast cancer, including genomic and transcriptomic characterization, treatment guidance, and resistance prediction. Molecular profiling of challenging entities such as early-onset breast cancer and HER-2 low tumours was summarized, with key findings highlighted. This review also discusses emerging technologies, including circulating DNA and single-cell sequencing, as promising avenues for discovery. CONCLUSION: NGS has revealed the genomic and transcriptomic diversity of breast cancer, identifying actionable alterations associated with chemotherapy response and resistance to therapies such as trastuzumab, TKIs, and CDK4/6 inhibitors. Circulating tumour DNA (ctDNA) shows potential for diagnosis, prediction, prognosis, and monitoring, despite tumour heterogeneity. Single-cell analysis enables exploration of individual cell transcriptomes, though high costs and low throughput remain barriers to widespread adoption. HER2-low tumours continue to pose significant research challenges.

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HumansBreast NeoplasmsHigh-Throughput Nucleotide SequencingFemalePrecision MedicineBiomarkers, TumorCirculating Tumor DNAGenomicsErb-b2 Receptor Tyrosine KinasesPrognosisSingle-Cell AnalysisHER-2 low breast cancerNext generation sequencingbreast cancercirculating tumour DNAsingle cell RNA sequencingJournal ArticleReviewResearch Support, Non-U.S. Gov't

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Nur Fatihah Mohd Zuhdi, Alaa Siddig, Siti Norasikin Mohd Nafi, Md Salzihan Md Salleh, Maya Mazuwin Yahya, Wan Zainira Wan Zain, Tengku Ahmad Damitri Al-Astani Tengku Din, Wan Faiziah Wan Abdul Rahman. 2025-10-06. Next-generation sequencing in breast cancer: current clinical applications and future directions.. https://doi.org/10.1080/07853890.2025.2569989

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