Abstract 2520: Analysis of the targeted sequencing with RNA Seq. results between primary breast cancer and metastatic sites: Matched paired analysis
Authors: Park Kyung Hee , Lee Eunjin , Park Seri , Lee Se Kyung , Kim Seok Won , Lee Jeong Eon , Nam Seok Jin , Kim Ji-Yeon , Ahn Hee Kyung , Park Woong-Yang , Park Yeon Hee 
Published: August 2019

Abstract
Background and Purpose In several breast cancer analyses of targeted gene panels, there was considerable concordance of mutations observed between primary tumors and matched metastases. We are to investigate to gain an understanding of the underlying genetics leading to BC metastasis to compare genomics data using paired biopsies between primary breast and several metastatic sites.
Methods We performed CancerSCANTM of forty-eight patients with paired primary and metastatic tumors, which is 380-gene targeted panel sequencing using HiSeq 2500 sequencing platform (Illumina). We made variant calls using Mutect for SNV, Pindel for INDEL, Contra for CNV, and in-house software for Fusion with default parameters. Tumor mutational burden (TMB) was measured by number of mutations per megabase (mb), and TMB was divided into two groups: high TMB (&gt;=20mutations/mb) and low TMB (&lt;20mutations/mb). Mutational signatures were estimated using R deconstructSigs package, and divided into high and low group by each signature’s median value. Twelve patients among this cohort were performed whole-transcriptome sequencing with TruSeq RNA prep kit (Illumina) on primary and/or metastatic fresh-frozen tumors.
Results Seven among 48 patients (14.6%) showed discordant subtypes between primary and metastatic tumors, discordant patterns were diverse. Lung and pleural was the most frequent organ in metastatic tumors, and liver and lymph node were followed. There were 15 shared, 6 primary-specific, 4 metastatic-specific mutations per patient on average, and no significant difference in overall survival (OS) with respect to mutation-sharing patterns. TMB and number of mutations related to mismatch-repair (MMR) genes such as NF1 (P=0.0398) and PMS2 (P=0.1020) tended to be reduced in metastatic tumors compared to paired primary tumors. Mutational signature 3 (BRCA1/2) was increased in metastatic tumors, and signature 5 (General Cancer) was decreased (P&gt;0.05). defect in MMR genes (P=0.0445) and germline BRCA mutation (P=0.0186) were significantly associated to OS, but TMB status, and mutational signature related to MMR respectively were not significant variables for OS according to the molecular profiles in primary tumors. Patients with PMS2 (P=0.156) and NF1 (P=0.0734) multi-hit mutations were better prognosis. Combining molecular profiles in primary tumors such as TMB and mutational signature 6 (MMR) and signature 13 (APOBEC) showed significant differences in OS: low TMB with high signature 6 plus 13 as worse, high TMB as intermediate, and low TMB with low signature 6 plus 13 as better prognosis (P=0.0228).
Conclusions With the combination of TMB and MMR-related molecular profiles, we could stratify patients into three groups according to OS.
Citation Format: Kyung Hee Park, Eunjin Lee, Seri Park, Se Kyung Lee, Seok Won Kim, Jeong Eon Lee, Seok Jin Nam, Ji-Yeon Kim, Hee Kyung Ahn, Woong-Yang Park, Yeon Hee Park. Analysis of the targeted sequencing with RNA Seq. results between primary breast cancer and metastatic sites: Matched paired analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2520.