Abstract: Background and Objectives: Phyllodes tumors are rare breast neoplasms with limited therapeutic options and poorly understood molecular characteristics. This study aimed to analyze genomic alterations and treatment outcomes in advanced phyllodes tumors using Japan's national clinical genomic testing registry (C-CAT database) to identify potential therapeutic targets and predictive markers. Materials and Methods: We conducted a retrospective analysis of 60 phyllodes tumor cases from 80,329 patients registered in the C-CAT database between June 2019 and August 2024. Comprehensive genomic profiling was performed using multiple platforms including FoundationOne CDx, NCC OncoPanel, and other approved tests. Treatment responses were evaluated according to RECIST criteria, and pathogenic variants were assessed using established databases including ClinVar and OncoKB. Results: The cohort's median age was 54 years (range: 13-79), with TERT promoter variants (70%), MED12 (52%), and TP53 (50%) mutations being the most frequent alterations. Forty patients received first-line chemotherapy, predominantly an-thracycline-based regimens (n=29). Although not reaching statistical significance, cases with CDKN2A and TERT alterations showed trends toward treatment resistance (OR>3.0). One patient with high tumor mutational burden (37/Mb) responded to pembrolizumab. Potential germline variants were identified in two cases (3.3%), involving MSH6 and TP53 alterations. Notably, no cases with CDKN2B alterations demonstrated treatment response (p=0.09). Conclusions: Our findings suggest distinct molecular patterns in phyllodes tumors compared to other soft tissue sarcomas, with potential implications for treatment selection. The identification of specific genetic alterations associated with treatment resistance may guide therapeutic decision-making, while the presence of actionable mutations in select cases indicates potential opportunities for targeted therapy approaches.

Fibroepithelial lesions (FL) of the breast, in particular Phyllodes tumors (PT) and fibroadenomas, pose a significant diagnostic challenge. There are no generally accepted criteria that distinguish benign, borderline, malignant PT, and FA. Combined genome-wide DNA methylation and copy number variant (CNV) profiling is an emerging strategy to classify tumors. We compiled a series of patient-derived archival biopsy specimens reflecting the FL spectrum and histological mimickers including clinical follow-up data. DNA methylation and CNVs were determined by well-established microarrays. Comparison of the patterns with a pan-cancer dataset assembled from public resources including "The Cancer Genome Atlas" (TCGA) and "Gene Expression Omnibus" (GEO) suggests that FLs form a methylation class distinct from both control breast tissue as well as common breast cancers. Complex CNVs were enriched in clinically aggressive FLs. Subsequent fluorescence in situ hybridization (FISH) analysis detected respective aberrations in the neoplastic mesenchymal component of FLs only, confirming that the epithelial component is non-neoplastic. Of note, our approach could lead to the elimination of the diagnostically problematic category of borderline PT and allow for optimized prognostic patient stratification. Furthermore, the identified recurrent genomic aberrations such as 1q gains (including MDM4), CDKN2a/b deletions and EGFR amplifications may inform therapeutic decision-making.