Goetz, Matthew P.

10513 Background: Prior reports of high frequency of BRCA1 and BRCA2 ( BRCA1/2 ) PVs among South Asian women from Bangladesh, India, Nepal, and Pakistan with breast or ovarian cancer require validation in large prospective unselected cohorts. Methods: Individual-level anonymized patient data from two prospective cohorts were pooled to evaluate the prevalence of germline PVs among South Asian women: the South Asian Regional Alliance for Hereditary Cancers (SARAH Consortium) in Bangladesh, Nepal, and Pakistan, and the previously reported Nurse-led Genetic Counseling and Awareness (NuGenA) expansion cohort in India. Both studies enrolled consecutive cases of histologically confirmed newly diagnosed breast or epithelial ovarian cancer irrespective of age at diagnosis or family history. In both studies, participants completed questionnaires on personal and family history (first-, second- or third-degree) and provided blood for germline genetic testing after written consent. PVs in cancer predisposition genes including ATM, BARD1, BRCA1, BRCA2, BRIP1, CHEK2, MLH1, MSH2, MSH6, PALB2, RAD51C, RAD51D, and TP53 were identified as part of the studies utilizing a multigene panel and the results were returned to ordering clinicians. The data cutoff date for this analysis was November 30, 2025. Results: The analysis included 1,711 South Asian women with breast (n=1,210) or ovarian (n=501) cancer. A family history of breast or ovarian cancer was noted in 177 (10.3%). Among breast cancers, 94% were invasive, 84% were ductal, 35% were triple-negative and over two-thirds presented with nodal involvement. Germline PVs across 13 predisposition genes were observed in 17.7% of breast and 35.9% of ovarian cancers. Notably, BRCA1/2 PVs accounted for most of these PV (13.6% of breast and 28.3% of ovarian cancer cases) with PVs in all genes except BRCA1/2 under 1%. The frequency of BRCA1/2 PVs was 24.4% in triple-negative breast cancer and 8.0% in ER+/HER2-. BRCA1/2 PV carriers were diagnosed with breast cancer at a younger age than non-carriers (Median age: 42 vs 46 years, P<0.001), with no age difference observed in ovarian cancer (50 vs. 51 years, P=0.79). Notably, among the 306 BRCA1/2 PV carriers identified, 229 (74.2%) did not report a family history of breast or ovarian cancer. Conclusions: We confirm a high prevalence of BRCA1/2 PVs among unselected South Asian women with either breast or ovarian cancer. The observations of younger age at cancer diagnosis, and low rates of family history support the need for population-specific germline genetic testing and risk management strategies in South Asia.

Abstract Background: The increasing volume and diversity of clinical genomic reports pose a significant challenge across healthcare institutions for the interpretation and proper implementation of precision oncology research. Reports from multiple different vendors (e.g., Invitae, Ambry Genetics, Foundation Medicine) are typically PDFs and exhibit substantial heterogeneity in panel design, gene coverage, and reporting standards, which hinders efficient retrospective data mining and patient cohort identification within the electronic medical records. We sought to develop a framework to interrogate all of these reports. Methods: We extracted genomic reports from patients with breast cancer treated with neoadjuvant chemotherapy and developed MolHarmonizer, a novel, scalable framework leveraging Python and Gemini LLMs, designed to process and harmonize genomic data from disparate multi-vendor reports. Gemini LLMs are employed explicitly for robust information extraction, normalization, and structuring of key genomic features, transforming unstructured data into a unified, queryable dataset. Results: Our MolHarmonizer framework successfully processed 1,147 genomic reports from 1703 breast cancer patients (2006-2023) from 23 different companies, demonstrating robust capability to extract and standardize critical actionable biomarkers. Data sources included Invitae (n=554), Ambry Genetics (n=189), Natera (n=95), Mayo Clinic (n=88), Tempus (n=63), Guardant Health (n=47), and Foundation Medicine (n=37), with others contributing less than 20 reports. Of the samples, 827/1147 (72.1%) were germline (blood/saliva). A majority of the patients were tested using the panels due to a personal/family history (n=925). Overall, 413/1147 (36.0%) reports identified at least one mutation. For breast cancer, 75 reports showed BRCA1/2 mutations (37 BRCA1, 37 BRCA2, and one patient with both BRCA1 and 2). Other mutations identified included: PIK3CA (n=40), TP53 (n=96), PTEN (n=21), ESR1 (n=13) and AKT1/2 (n=8). Conclusion: MolHarmonizer, a powerful framework leveraging Gemini LLMs, effectively addresses genomic data heterogeneity by automating biomarker extraction and harmonization. This enables rapid cohort identification and deep retrospective analyses for clinical insights, biomarker discovery, understanding disease history, facilitating novel pattern discovery, e.g., predicting BRCA1 mutations from WSI, and accelerating research within our neoadjuvant BC cohort. Future plans include expanding to include over 20,000 breast cancer patients, developing a user-friendly chatbot, and ensuring inter-institutional adaptability for a variety of complex diseases. Citation Format: Krishna Rani Kalari, Xiaojia Tang, Thanmayee Boyapati, Tanya L. Hoskin, Sumathilatha Myla, Sumedha G. Penheiter, Richard M. Weinshilboum, Liewei Wang, Hamid R. Tizhoosh, Karthik Vikram Giridhar, Matthew P. Goetz, Judy C. Boughey. Development of an LLM framework for analysis of heterogeneous breast cancer patients genomic reports [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2756.