Abstract 984: Implementation of tissue next generation sequencing in a real world diverse safety-net setting
Authors: Kavya Athipatla, Lindsay C. Reynolds, Susmita Potti, Mitchell S. von Itzstein, Janet Miles, Kalyani Narra
Journal: Cancer Research (2025)

Abstract Background: Next-generation sequencing (NGS) is generally considered the standard of care for molecular testing in advanced cancer cases across professional organization guidelines. Implementing expensive NGS testing in safety-net settings poses significant challenges due to limited resources. John Peter Smith Health Network (JPS) serves a large diverse population of uninsured and underinsured patients, and we addressed this challenge by partnering with ProPath and Bernhardt Laboratories (BHL) to facilitate tissue NGS testing. Methods: Patients at JPS with tissue NGS tested between 1/1/24 to 9/30/24 using a ProPath authorization program and BHL testing were included. AuraSeq-Comprehensive was the NGS test utilized and includes a panel detecting clinically relevant alterations in 500 cancer-related genes, including base pair substitutions, small insertions and deletions, copy number variations, and gene fusions. Data analysis was performed using Excel. Results: A total of 152 patients underwent tissue analysis, each patient undergoing a single NGS test during this period. The average age was 62 years and there were 76 (50%) females. 41 (27%) were Hispanic, 54 (36%) non-Hispanic White, 41 (27%) non-Hispanic Black, 16 Asians and others. Excluding tumor mutational burden (TMB), homologous recombinant deficiency (HRD) and Microsatellite instability (MSI), 146 patients had at least one genomic alteration, 118 had two, 87 had three, 55 had four, and 26 had five. TMB testing was conducted on 150 patients and 29 (19%) had high TMB using a cutoff of 10 mut/Mb. HRD testing was positive in 14 out of 150 (9%). MSI was high in 2 out of 15 tested. A total of 5 (10%) ALK fusions, 10 (21%) activating EGFR alterations, 1 (2%) MET exon 14 skipping mutation, and 9 (19%) KRAS G12C mutations were noted in 48 non-squamous NSCLC cases. Of the 9 Hispanic patients with non-squamous NSCLC, 2 had ALK fusions, 3 had EGFR mutations and 1 had KRAS G12C. Of the 21 patients with squamous NSCLC, one patient had BRAF mutation. Of the 43 patients with gastrointestinal cancers, there were 1 KRAS G12C, 2 BRAF, 1 BRCA2, 2 ERBB2 amplifications. Of the 13 breast cancers, there were 3 PIK3Ca, 1 BRCA2, 1 ERBB2 amplification and 1 ERBB2 alterations. JPS enrolled the nationwide 1st patient on PrE1702 Real-World Data Study in October 2024 and has opened clinical trials for patients with KRAS and PIK3Ca alterations. Conclusions: This study demonstrates the successful implementation of NGS in a safety-net healthcare setting through public-private partnership. Our analysis revealed a high prevalence of actionable genomic alterations across various cancer types, with significant findings in non-squamous NSCLC, especially among Hispanic patients. Future efforts should focus on expanding access to genomic testing to further improve patient care and outcomes with opportunities for more clinical trials in safety-net settings. Citation Format: Kavya Athipatla, Lindsay C. Reynolds, Susmita Potti, Mitchell S. von Itzstein, Janet Miles, Kalyani Narra. Implementation of tissue next generation sequencing in a real world diverse safety-net setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 984.