Comprehensive genomic profiling of Taiwanese triple negative breast cancers with medium- and large-sized sequencing panels: a comparative study of actionable genes

Author:

Huang Chi-Cheng1,Yeh Yi-Chen1,Tsai Yi-Fang1,Lin Yen-Shu1,Chao Ta-Chung2,Liu Chun-Yu2,Ho Hsiang-Ling1,Tseng Ling-Ming1

Affiliation:

1. Taipei Veterans General Hospital

2. National Yang Ming Chiao Tung University

Abstract

Abstract

Introduction: 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, however, how large a panel should be used for breast cancer remains undetermined. Methods Triple negative breast cancer (TNBC) patients from the VGH-TAYLOR study were initially assayed by a medium-sized CGP panel (Oncomine Comprehensive Panel, OCP, v3), and the remaining nucleic acid specimens were re-sequenced with a large-sized CGP panel (TruSight Oncology 500, TSO500). Molecular profiling between the two sequencing panels was compared and reported. Results A total of 108 breast cancers were successfully assayed using both platforms and 272 variants were reported at least once by OCP or TSO500. Variants reported were among actionable genes (AKT1, BRCA1/2, PALB2, ERBB2, PIK3CA, PTEN) and TP53. Concordance rate between TSO500 and OCP was 34.6% and was enhanced to 58.9% after excluding polymorphisms, out-of-targeted region variants and those with low variant allele frequency (< 10%). Conclusion Only one-third of actionable mutations could be detected consistently between the medium- and the large-sized CGP panels using the default analytical pipelines, while extensive bioinformatics analyses improved variant calling consistency substantially. TSO500, the larger panel, detected more variants than OCP from the same set of actionable genes.

Publisher

Springer Science and Business Media LLC

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