Overview of next-generation sequencing to the molecular diagnosis of inborn errors of immunity in Brazil: a systematic review

Background Inborn errors of immunity (IEI) are rare monogenic disorders affecting the immune system, leading to immunodeficiency, autoinflammation, autoimmunity, allergy, and/or malignancy. The identification of IEI has accelerated with next-generation sequencing (NGS), increasing the molecular diagnostic rate. In Latin America, IEI prevalence is about 1 in 10, 000 individuals. However, the limited availability of NGS in Brazil delays early diagnosis, personalized therapeutic interventions, and comprehensive genetic counseling. To our knowledge no systematic review has yet aimed to summarize the Brazilian studies employing NGS methodologies for the genetic diagnosis of IEI. Methods This review was conducted in accordance with PRISMA guidelines and is registered with PROSPERO (CRD420251059458). A comprehensive systematic search of Embase, MEDLINE, SciELO and LILACS databases was performed to identify studies published up to April 2025. Inclusion criteria were restricted to Brazilian studies reporting on native patients diagnosed with IEI that employed NGS methodologies. Results From 242 studies initially found, 10 studies filled the inclusion criteria, comprising six case reports and four case series, reporting data from 419 patients, of whom 82 were diagnosed with IEI (19.6%), the majority of whom were diagnosed with SCID, CGD, and XLA. The studies were conducted in the Southeast, Northeast, and South regions of Brazil, which evidences a lack of studies in the North and Middle-West Brazilian regions. Considerable variability was observed among studies in reporting methodological details of NGS workflows, including sequencing platforms, bioinformatics pipelines, and quality control metrics. Although strategies based on WES predominated, platform specifications were often incomplete or omitted. Bioinformatic workflows were inconsistently detailed, with variable reporting of alignment tools, reference genomes, variant callers, and annotation software. Quality control metrics and thresholds lack standardization, limiting comparability. Variant prioritization and interpretation approaches varied, though ACMG/AMP guidelines were generally followed when reported, highlighting the need for standardized, transparent pipelines to improve reproducibility and diagnostic accuracy. Conclusion The findings of this systematic review reveal few Brazilian studies employing NGS for IEI diagnosis. Limited utilization hinders early subtype identification and clinical management of patients. Large multicentric studies covering all regions and standardized reporting are needed to inventory IEI epidemiology and guide national diagnosis policies. Systematic review registration https://www.crd.york.ac.uk/prospero/ , identifier CRD420251059458.