PP475 Paired targeted genomic profiling of triple-negative breast cancer to identify novel mutations in residual disease

Abstract

Background Patients with residual disease after neoadjuvant chemotherapy (NACT) in triple-negative breast cancer (TNBC)have a significantly worse prognosis as compared to patients who have a complete pathological response. Residual disease is treated with capecitabine or olaparib (if germline BRCA mutation is present). We planned this study to identify new somatic alterations in the residual disease that were not present at the diagnosis that can potentially be targeted. Methods Patients diagnosed with TNBC and planned for treatment with NACT followed by surgery were eligible for this study. DNA was retrieved from archived formalin-fixed paraffin-embedded tissue (FFPE) blocks from the baseline biopsy tissue and the final surgical specimen. DNA was extracted from both FFPE blocks using QIAGEN kits. DNA sequencing was performed using Illumina Novaseq 6000 at a target depth of 300X to cover a custom-made panel of genes. A blood sample was also collected to perform germline testing. Inhouse bioinformatic pipelines were developed to analyze data from all three samples. Results We identified 36 patients with TNBC who received NACT from July 2023 to December 2023. Of these, 17 were excluded due to inadequate baseline or residual tissue DNA. Of the 19 patients, 10 had a pathological complete response, and 9 had residual disease. Of these, sequencing data from 5 pairs passed the quality check. In all 5 residual tumor tissues, a median of 1257 (range, 483-4757) new genetic alterations were observed that were absent in the germline or baseline biopsy samples. Across the 5 residual tissues, we identified 679 common missense variants. After eliminating variants with no deleterious effect using insilico tools, we found 2 deleterious mutations not present in the biopsy developed after NACT: OTC:A208T and RAG1:R759C. Conclusions We found two novel mutations in the residual disease that were absent before NACT administration. Further functional assays would be needed to validate these findings. However, these findings support the hypothesis that novel mutations develop after the administration of chemotherapy that can drive resistance to such therapy and may act as novel targets for new drug development.