The implementation of next-generation sequencing (NGS) in a Brazilian public hospital: a systematic review of challenges and perspectives in oncology

Next-generation sequencing (NGS) technology has revolutionized oncology by detecting novel and rare somatic cancer mutations and identifying individuals with pathogenic germline variants, both of which can facilitate personalized medicine. By integrating NGS into routine diagnosis in Brazil, patients may benefit from improved treatment responses, however, several barriers to the implementation of NGS in Brazil exist. This review provides practical insights into how NGS can be integrated into diagnostics in public hospitals. A comprehensive systematic review was conducted following the guidelines of the Preferred Reporting Items for Systematic Review and Meta Analysis (PRISMA). PubMed, Medline, and Cochrane databases were queried for publications written in English, French, Portuguese, or Spanish from 2014 to February 2025. The research was conducted using Medical Subject Headings (MeSH), including terms such as NGS, public hospital, diagnostic, implementation and Brazilian Public Health System (SUS). Of the 7,804 articles identified, 1,233 were analyzed with only 10 meeting inclusion criteria. Current literature on NGS is largely centered in the Global North, with limited contributions from low- and middle-income countries. Key challenges included lack of access to molecular profiling and inadequate medical education (27% each), high costs of NGS (23%), data interpretation challenges (15%), and need for additional cost-benefit analyses (8%). Of note, only one paper conducted a cost-effectiveness analysis, demonstrating the utility of NGS in treating cancer. This systematic review highlights key gaps on NGS implementation in Brazil. There is a need for improved education for healthcare professionals and students to effectively incorporate NGS into clinical oncology practice, as well as strategies to lower costs of sequencing and systematic data interpretation pipelines. Despite these challenges, Brazil has the potential to lead NGS implementation in Latin America. Our experiences at a public hospital may be used as a model to implement NGS through meticulous procurement management, leveraging expertise from basic research, and integrating AI-driven data analysis platforms.