Targeted Next-Generation Sequencing for Improved Clinical Outcomes in People Living With Rare Diseases in Global South: Protocol for a Systematic Review and Meta-Synthesis

BACKGROUND Rare diseases affect many individuals and pose major challenges in diagnosis and treatment, especially in Global South countries where health care resources are limited. Targeted next-generation sequencing (NGS) has significantly advanced diagnostic accuracy and clinical care for rare diseases globally; however, its implementation and impact within the Global South context remain insufficiently studied. OBJECTIVE This study aims to evaluate the use, clinical benefits, challenges, and implementation outcomes of targeted NGS for diagnosing and managing rare diseases in Global South populations. Specifically, it seeks to quantify the diagnostic yield of NGS, examine its influence on subsequent clinical decision-making, and identify principal barriers to, and facilitators of, the implementation of targeted NGS approaches in these contexts. METHODS This protocol follows the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. We will systematically search PubMed, Scopus, and Web of Science for studies published between 2005 and 2025 that report on the use of targeted NGS in Global South population with rare diseases. Two reviewers will independently perform study selection, data extraction, quality assessment, and evaluation of risk of bias by using QUADAS-2 for diagnostic accuracy studies and the risk of bias assessment tool for nonrandomized studies. Meta-analyses will be conducted to estimate pooled outcomes for diagnostic yield, with heterogeneity assessed using random effects models. Heterogeneity will be further examined through visual inspection of forest plots and by evaluating the chi-square test and I² statistic. RESULTS The protocol has been registered with PROSPERO (CRD420251078455). Database search or screening, data extraction, and data synthesis are planned to commence in June 2026 and conclude by September 2026. Study findings will synthesize the diagnostic yield, clinical impact, and contextual determinants influencing the implementation of targeted NGS in Global South health care settings. CONCLUSIONS This review will provide evidence on the application, advantages, limitations, and clinical outcomes of targeted NGS for individuals affected by rare diseases in countries of the Global South. The finding will identify priorities for capacity strengthening, policy development, and future genomic research. CLINICALTRIAL PROSPERO CRD420251078455; https://www.crd.york.ac.uk/PROSPERO/view/CRD420251078455 INTERNATIONAL REGISTERED REPORT PRR1-10.2196/85150