Comprehensive genomic profiling of Taiwanese triple‑negative breast cancer samples with medium‑ and large‑sized sequencing panels: A comparative study implicating treatment allocations

Comprehensive genomic profiling (CGP) is a molecular diagnostic tool with increasing use in cancer research and treatment. There are several commercialized CGP assays with variable targeted genes, while the differences between medium- and large-sized panels in refining genomic profiling strategies, optimizing resource allocation and enhancing clinical applications require evaluation. In the present study, patients with triple-negative breast cancer (TNBC) from the Veterans General Hospital TAipei-Yung-Ling foundation sinO-canceR study were initially assayed using a medium-sized CGP panel (Oncomine comprehensive panel), and the remaining nucleic acid specimens were re-sequenced with a large-sized panel (TruSight Oncology 500). The molecular profiling between the two sequencing panels was compared. A total of 108 breast cancer samples were successfully assayed using both platforms and 272 variants were reported at least once by either type of CGP. The reported variants were among actionable genes (<i>AKT1</i>, <i>BRCA1/2</i>, <i>PALB2</i>, <i>ERBB2</i>, <i>PIK3CA</i> and <i>PTEN</i>), which can be acted upon or have clinical relevance for therapeutic intervention and <i>TP53</i>. The concordance rate between the medium- and large-sized panels was 34.6%, which was enhanced to 58.9% after excluding polymorphisms, out-of-targeted region variants and those with low variant allele frequency (#x003C;10%), with variants of <i>TP53</i>, <i>ERBB2</i> and <i>PTEN</i> being mostly enhanced. A majority of discordance came from TruSight Oncology 500-detected only variants, especially <i>BRCA1</i>, <i>BRCA2</i> and <i>PALB2</i>. In conclusion, the results indicated that only one-third of actionable mutations could be detected consistently between the medium- and large-sized CGP panels using the default analytical pipelines, while extensive bioinformatics analyses improved concordance substantially. The large-sized panel detected more variants, thereby enhancing clinical actionability. With more therapeutic targets revealed in the future, CGP may be particularly impactful in refining strategies for TNBC management.