Next-Generation Sequencing (NGS) has revolutionized molecular diagnostics by enabling simultaneous analysis of hundreds or thousands of genes across diverse clinical applications. These include germline testing for hereditary disorders, somatic mutation profiling in oncology, infectious disease characterization, and transcriptomic gene expression analysis.
A particularly impactful advancement is liquid-biopsy NGS, which allows non-invasive detection of tumor-derived nucleic acids—such as circulating tumor DNA (ctDNA) or RNA—from blood or other bodily fluids. This method now supports cancer screening, minimal residual disease monitoring, and therapy stratification.
NGS also powers Comprehensive Genomic Profiling (CGP). These assays assess a wide spectrum of biomarkers—single nucleotide variants (SNVs), insertions and deletions (indels), copy number alterations (CNAs), copy number losses (CNLs), gene fusions, and splicing events—across large panels in a single run. Many workflows also integrate microsatellite instability (MSI) and tumor mutational burden (TMB).
Assays can range from targeted panels to whole exome sequencing (WES) or whole genome sequencing (WGS). Each format carries unique validation needs and bioinformatics requirements. The mix of technologies, analytes, sample types (e.g., blood, plasma, FFPE, cfDNA, RNA), and clinical contexts increases regulatory complexity.
Under the EU In Vitro Diagnostic Regulation (IVDR; EU 2017/746), you must define each intended use clearly and support it with comprehensive evidence of scientific validity, analytical performance, and clinical performance. That requirement calls for a holistic, coordinated validation and documentation strategy.
For CE-marking manufacturers and clinical laboratories operating under Article 5(5), IVDR demands structured validation, clear documentation, and lifecycle management. For NGS-based assays, compliance becomes even more demanding due to scientific, technical, and operational intricacies.
Key Challenges in IVDR Compliance for NGS
1) Complex Gene Panels & Variant Diversity
NGS panels often include multiple genes and variant types, each with distinct performance characteristics. You must demonstrate analytical performance—sensitivity, specificity, LoD, and robustness—per variant class. This tailoring increases the scale and complexity of testing.
2) Defining a Clear Intended Use
A precise, testable intended purpose statement anchors the program. Define analytes, clinical context, sample types, output format, and role in patient care. Any ambiguity risks misclassification or validation gaps.
3) Scientific Validity Across Many Analytes and Conditions
Establishing scientific validity grows challenging when one test targets dozens or hundreds of genes. Under IVDR, link each analyte to a clinically relevant condition. That linkage often requires extensive literature review, database referencing, and written justification for inclusion.
4) Clinical Performance Evidence
With broad genomic scope, comprehensive clinical studies may be infeasible. A pragmatic approach combines routine diagnostic data, published literature, and a clear link to Post-Market Performance Follow-up (PMPF) plans to support claims over time.
5) Complex Bioinformatics Pipelines
Bioinformatics sits at the core of NGS diagnostics. Validate every step—from base calling to variant annotation. Implement version control, clear revalidation triggers, and change management to maintain consistent performance after software updates.
6) Use of Third-Party Reagents and Instruments
NGS workflows often incorporate off-the-shelf reagents and platforms not originally CE-marked as part of the IVD system. Document compatibility, performance, and traceability of third-party components to meet IVDR expectations.
7) Labelling Without a Physical Device
Many NGS assays function as software-driven services or LDTs without a packaged device. You still must meet Annex I labelling and Instructions for Use (IFU) requirements—even without physical labels or packaging.
How MDx CRO Supports Your IVDR Journey
MDx CRO brings specialized expertise to guide NGS programs through IVDR across the full lifecycle:
- Gap Assessments: Identify regulatory shortfalls and prioritize remediation.
- Performance Evaluation Plan (PEP): Craft PEPs that balance analytical rigor with operational feasibility.
- Analytical Study Oversight: Design statistically robust studies tailored to complex panels.
- Bioinformatics Validation: Map and validate each software component under IEC 62304 and ISO 13485.
- QMS Integration: Build audit-ready documentation, risk management, and traceability.
- PMS & PMPF Strategies: Establish real-world evidence systems that sustain compliance and support clinical claims.
Conclusion
Achieving IVDR compliance for NGS assays poses a multi-dimensional challenge that blends regulatory discipline with scientific depth. From defining intended use to managing software changes and clinical claims, every step benefits from clarity, structure, and foresight.
MDx CRO partners with diagnostics developers and clinical laboratories to turn regulatory complexity into actionable validation strategies—accelerating time to market while protecting long-term compliance and patient safety.
