Ensuring Precision in Genetic Testing: Advancing Quality Standards for Rare Neurological Diseases

Next-generation sequencing (NGS) has transformed genetic diagnostics, particularly in addressing the challenges posed by rare neurological diseases (RNDs). These disorders often exhibit extensive genetic heterogeneity and overlapping clinical features, making accurate diagnosis critical for effective patient care. In this context, the European Reference Network for Rare Neurological Diseases (ERN-RND) has taken significant strides to standardize and ensure the quality of NGS diagnostics across Europe, as highlighted in a recent article published in the European Journal of Human Genetics.

The Need for Quality Standards
NGS-based diagnostics, including exome and genome sequencing, have become indispensable tools in identifying the molecular underpinnings of RNDs. However, variations in sequencing techniques, bioinformatics pipelines, and reporting standards have led to inconsistencies in diagnostic outcomes. This variability underscores the urgent need for harmonized guidelines to improve diagnostic accuracy, reproducibility, and patient safety.

Establishing an External Quality Assessment Scheme
In collaboration with the European Molecular Genetics Quality Network (EMQN), ERN-RND developed an external quality assessment (EQA) scheme to evaluate laboratory performance in NGS diagnostics. The initiative began with a pilot in 2021 involving 29 laboratories, followed by a broader implementation in 2022 with 42 participants. Labs were tasked with analyzing DNA samples from hypothetical cases, focusing on genotyping, variant interpretation, and reporting.

Key findings included:
A majority of labs used exome or genome sequencing.
Performance was assessed based on genotyping accuracy, interpretative standards, and clerical precision.

Insights into Laboratory Practices
The EQA revealed significant variability in diagnostic approaches:
Technology: Most labs employed in-house bioinformatics pipelines for data analysis.
Validation: While some labs consistently confirmed results using Sanger sequencing or MLPA, others relied solely on NGS data.
Reporting: Discrepancies were noted in the inclusion of quality parameters, such as coverage and methodology details, in diagnostic reports.

Challenges in Variant Interpretation
Accurate variant interpretation remains a critical aspect of NGS diagnostics. The study highlighted:
Inconsistent use of established guidelines like ACMG (American College of Medical Genetics).
Errors in interpreting variants’ clinical relevance, with some labs misclassifying variants due to incomplete evidence or reliance on unverified databases.
Improved adherence to interpretation standards in 2022 compared to 2021, but significant gaps persist.

Addressing Clinical Relevance and Reporting
The evaluation of clinical reports revealed variations in:
Linking molecular findings to clinical presentations.
Providing actionable recommendations, such as recurrence risks and genetic counseling.
Report clarity and length, with some exceeding five pages and overwhelming the target audience.

Recommendations for Harmonization
To address these challenges, the authors proposed:
Standardizing Reporting: Include clear statements on methodology, quality metrics, and clinical relevance.
Enhancing Training: Promote adherence to ACMG guidelines and ensure evidence-based variant classification.
Developing Best Practices: Create tailored guidelines for RND diagnostics to address unique challenges, such as detecting complex structural variants.

Conclusion
The ERN-RND's EQA scheme represents a pivotal step toward harmonizing NGS diagnostics for RNDs in Europe. By fostering collaboration, developing robust standards, and continuously evaluating laboratory practices, the network aims to improve diagnostic accuracy and patient outcomes. As the adoption of genome sequencing expands, these efforts will play a crucial role in setting a global benchmark for NGS-based diagnostics.

References:
Maver, A., Lohmann, K., Borovečki, F. et al. Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network. Eur J Hum Genet 32, 1014–1021 (2024).