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Background  Breast cancer is one of the leading causes of cancer-related deaths in women, and there is a demand in developing an Asian-based genetic profiling database for breast cancer in improving the treatment response. This study aimed to determine molecular alternations and identify potential therapeutic targets by analyzing the genetic profiling from a cohort of Taiwanese breast cancers using a commercialized next-generation sequencing (NGS) targeted panel.    Methods  The study population comprised a broad spectrum of breast cancer patients in Taiwan, including Group 1: planned to receive first-line surgery and followed by adjuvant therapy, or early relapse within three years, Group 2: planned to receive first-line neoadjuvant therapy and followed by surgery, and Group 3: de novo stage IV, or stage IV with recurrence beyond three years. Molecular profiles were determined using Thermo Fisher™ Oncomine™ Comprehensive Assay version 3 (TMO comprehensive assay) from Formalin-Fixed Paraffin-Embedded (FFPE) tissues. Level of actionability was evaluated with the ESMO Scale of clinical actionability of molecular targets (ESCAT).    Results  A total of 380 TMO comprehensive assays were conducted on 372 patients, and we presented targeted sequencing analyses of Tier I: alteration-drug match associated with improved outcome in clinical trials including  ERBB2  amplification,  BRCA1/2  germline mutation,  PIK3CA  mutation, and  NTRK  translocation, and Tier II: antitumor activity associated with the matched alteration-drug but lack of prospective outcome data including  PTEN  loss,  ESR1  mutation,  AKT1  mutation, and  ERBB2  mutation, and Tier III: matched drug-alteration that led to clinical benefit in another tumor type including  MDM2  amplification, and  ERBB3  mutation. Among them, 249 (66%) showed at least one actionable alternation based on the ESCAT criteria. The most frequent impacted genes (all variants combined within each sample) were  PIK3CA  (38%), followed by  ERBB2  (23%),  ESR1  (10%),  AKT1  (6%), and  BRCA2  (5%), and the remaining rare variants (less than 5% of assayed cohort) were  BRCA1  (3%),  MDM2  (2.2%), and  ERBB3  (1.1%).    Conclusion  Targeted sequencing of actionable genes is believed to provide clinical applicability and substantial benefits for Taiwanese breast cancer patients. A valid scale of clinical actionability should be adopted for precision medicine practice under multidisciplinary molecular tumor board.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12885-021-07931-4.

bmc cancer

Comprehensive molecular profiling of Taiwanese breast cancers revealed potential therapeutic targets: prevalence of actionable mutations among 380 targeted sequencing analyses