Molecular Test Distinguishes Ipsilateral Second Primary from Recurrent Breast Cancer An interview with: Tess Snellen MSc, Netherlands Cancer Institute – Antoni van Leeuwenhoek hospital, Department of Surgical Oncology, Amsterdam, The Netherlands. BARCELONA, Spain—A molecular test using next generation sequencing has proved able to distinguish swiftly, and with great accuracy, the recurrence of a patient’s ipsilateral breast cancer from a completely new primary tumor. The 2026 European Breast Cancer Conference heard findings from researcher Tess Snellen from the Netherlands Cancer Institute in Amsterdam, who then talked with our reporter, Peter Goodwin: AUDIO JOURNAL OF ONCOLOGY: Tess Snellen MSc EBCC 2026 ABSTRACT: Distinguishing True Recurrence from Second Primary Breast Cancer by Molecular Clonality Analysis Snellen1,, E. Lips2,, L. Bosch3,, T. Wiersma4,, A. Scholten4,, M. Noë5,, M.J. Vrancken Peeters6,, V. Dezentjé7,. 1Netherlands Cancer Institute – Antoni van Leeuwenhoek hospital, Department of Surgical Oncology, Amsterdam, The Netherlands. Background A second breast cancer (BC) in the ipsilateral breast or regional lymph nodes may be a true recurrence (TR) or second primary (SP) tumor. This distinction is clinically relevant, as TRs are associated with a poorer prognosis and require a more challenging therapeutic approach compared to SPs. The aim of this study was to describe the findings and success rates of molecular clonality analysis (MCA) techniques used to distinguish a second ipsilateral BC as either a TR or a SP. In addition, a comparison between a MCA-based and a clinicopathological classification was made. Material and methods Through electronic patient files and pathology reports, data were collected from a historical cohort of patients who underwent MCA for a second ipsilateral locoregional BC at the Netherlands Cancer Institute between 2000 and 2024. The primary objective was to describe the findings and success rates of the different MCA techniques. The secondary objective was to compare molecular with clinicopathological classification using the Jobsen Morphology method. Results In total, 85 patients were included, in whom 99 MCAs were performed. Before 2017, all MCA involved loss of heterozygosity (LOH) analysis (100%), hereafter, targeted next-generation sequencing (NGS) panel analysis and copy number variation (CNV) analysis were introduced. After 2017, targeted NGS panel analysis was most frequently applied (65.4%), followed by CNV (18.5%) and LOH analysis (16.0%). CNV analysis had the highest success rate (93.3%) yielding the most conclusive MCA results, followed by targeted NGS panel (73.6%), and LOH analysis (61.3%) (table 1). Of the 99 MCAs, 40.4% tumor pairs were classified as clonally related, 10.1% as likely clonally, 22.2% as not clonally related, 27.3% were inconclusive. A substantial discordance (29.6%) was observed between the MCA-based classification and Jobsen Morphology method, with clinicopathological assessment showing limited predictive value for MCA-determined TRs (PPV 78.7%, NPV 22.2%). Conclusion In conclusion, we demonstrate that MCA, especially targeted NGS panel and CNV analysis, is successful in distinguishing TRs from NPs. Clinicopathological classification using the Jobsen Morphology method however has limited value in predicting clonal relatedness. Therefore, we recommend implementing MCA in the diagnostic workup of second ipsilateral BC when the outcome may influence therapeutic decision-making, as part of a tailored treatment approach for BC recurrence. 260325 Tess Snellen EBCC 2026 Audio Journal of Oncology

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