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Brazilian systematic review reveals NGS diagnostic rates and reporting gaps for inborn errors of immunity across regionsNext-generation sequencing helps diagnose immune disorders in Brazil but reporting varies widely

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Key Takeaway
Standardized NGS reporting and regional coverage are critical for improving inborn errors of immunity diagnosis and management in Brazil.

This systematic review analyzed 419 Brazilian patients diagnosed with inborn errors of immunity to evaluate the impact of Next-Generation Sequencing methodologies. The analysis included six case reports and four case series, revealing that 82 patients received a molecular diagnosis. The majority of identified conditions involved severe combined immunodeficiency, chronic granulomatous disease, and X-linked agammaglobulinemia. Despite these successes, the study highlights a critical lack of standardized reporting across different Brazilian regions.

Significant variability was observed in how studies reported NGS workflow details. Many publications omitted specific sequencing platform specifications or failed to detail bioinformatic pipelines. This inconsistency includes variable reporting of alignment tools, reference genomes, and variant callers. Furthermore, quality control metrics and thresholds lack standardization, which severely limits the comparability of results between different centers. Such gaps hinder the ability to draw robust conclusions about diagnostic performance across the country.

Regional distribution of studies showed a concentration in the Southeast, Northeast, and South regions, with a notable absence of research in the North and Middle-West. Variant prioritization approaches varied, although ACMG/AMP guidelines were generally followed when reported. These limitations suggest that limited availability of NGS delays early diagnosis and personalized therapeutic interventions. Large multicentric studies covering all regions are needed to inventory epidemiology and guide national diagnosis policies effectively.

Many children in Brazil live with rare immune disorders called inborn errors of immunity. These conditions can be hard to spot without the right tools. A new review looked at how 419 patients diagnosed in Brazil were tested. The study found that next-generation sequencing helped identify 82 of these patients. This technology reads genetic code to find the specific cause of the illness. Most of the diagnosed cases involved severe combined immunodeficiency, chronic granulomatous disease, or X-linked agammaglobulinemia. These are serious conditions that weaken the body's defense system.

However, the way researchers reported their testing methods was not consistent. Details about the machines used, the computer programs that analyzed the data, and the quality checks performed varied greatly. Some studies did not even list the specific tools they used. This makes it difficult to compare results from different hospitals or regions. The review noted that studies were mostly done in the Southeast, Northeast, and South parts of the country. No studies were found in the North or Middle-West regions.

Because the reporting was so varied, it is hard to know exactly how well the tests work everywhere. Without standard rules for how to report these tests, doctors cannot easily share what they learned. This gap in information could delay finding the right treatment for patients who need it most. The review suggests that larger studies with consistent reporting are needed to improve care across the nation.

What this means for you:
Next-generation sequencing diagnoses immune disorders in Brazil, but inconsistent reporting limits comparison and care.

Study Details

Study typeMeta analysis
EvidenceLevel 1
PublishedMay 2026
View Original Abstract ↓
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. 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. 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. 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. https://www.crd.york.ac.uk/prospero/, identifier CRD420251059458.
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