Comprehensive genomic profiling of Taiwanese patients with breast cancer using a novel targeted panel: Preliminary analyses from a prospective triple-negative cohort.

Abstract

e12553 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 to improve treatment outcomes. This study aims to determine the molecular alterations and identify potential therapeutic targets from a cohort of Taiwanese triple negative breast cancers using a novel next-generation sequencing (NGS) targeted panel. Methods: The VGH-TAYLOR study was designed to understand the genetic profiling of different subtypes of breast cancer in Taiwan. The study population comprised both early- (first-line surgery or neoadjuvant therapy) and late-stage (early/late relapse or de novo stage IV disease) of breast cancers, and we conducted molecular profiling with the illumina TruSight Oncology 500 assay using both DNA and RNA extracted from FFPE tissues from a subset of 101 prospectively enrolled breast cancers, which were previously assayed with a commercialized panel of 161 genes. Results: A total of 100 breast cancers from VGH-TAYLOR study were successfully assayed, with the majority (n = 97) being triple-negative, two HER2 over-expressed and the remaining one being HER2-low phenotypically. The most prevalent actionable alterations (more than 5% of study cohort) came from BRCA2 (24%), BRCA1 (12%), PALB2 (5%), PIK3CA (38%, both mutations and amplifications), ERBB2 (14%, both mutations and amplifications), ERBB3 (10%) and PTEN (12%). One-quarter of assayed samples were categorized into tumor mutation burden (TMB)-high cancers ( > 10 mutations per million bases), which came from 15 out of 74 (20%) early-stage and 10 out of 26 (38%) late-stage patients (chi-square test p-value: 0.06). In general, the novel panel with 500 targeted genes reported more actionable alterations than the former one with limited interrogated genes ( BRCA2: 7%, BRCA1: 12%, PALB2: 7%, PIK3CA: 45%). Conclusions: Our study ascertained the clinical applicability and feasibility of comprehensive genomic profiling from a cohort of Taiwanese breast cancers. Overall, the successful rate for NGS with QC metrics are around 90%. The novelty benefits from more investigated genes as well as multi-gene biomarkers such as TMB and microsatellite instability (MSI) status. Patients with a positive finding from the genomic assay may benefit from an immune checkpoint inhibitor (TMB-high and MSI), poly ADP- ribose polymerase (PARP) inhibitor (homologous recombination deficiency genes: BRCA1/2 and PALB2), selective estrogen receptor degrader ( ESR1), tyrosine kinase inhibitor ( ERBB2/3), phosphoinositide 3-kinase inhibitor ( PIK3CA) and so on. Further studies with more samples enrolled and longer follow up are warranted to elucidate the true value of comprehensive genomic profiling for breast cancer.