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NGS Made Practical: Meeting European Pharmacopoeia Standards with Genedata Selector

March 30, 2026

New Ph. Eur. 2.6.41 Chapter Aims to Accelerate NGS Adoption for Quality Control   

Implementing next-generation sequencing (NGS) for adventitious agent detection is becoming more practical, driven by new guidance from the European Pharmacopoeia in general chapter Ph. Eur. 2.6.41, published in Issue 12.1 Issued by the European Pharmacopoeia Commission (EPC), the chapter clarifies regulatory expectations for NGS-based adventitious viral detection and provides a clearer framework for integrating NGS into quality control workflows that support the delivery of safe biotherapeutics.  

Meeting these regulatory standards places greater emphasis on the robustness, reproducibility, and traceability of NGS methods across validation-ready and regulated contexts. As a result, biopharma organizations can benefit from validation-ready NGS analysis software to accelerate adoption while maintaining effective quality control frameworks. Genedata Selector® is a GxP-validation-ready NGS data analysis solution that enables biopharma and biotech organizations to operationalize these guidelines through compliant, scalable NGS workflows for quality control.

Highlights of the New General Chapter

Delivering Broad Viral Detection and 3R Compliance: Why NGS Is the New Standard

The new general chapter of the European Pharmacopoeia positions NGS as a highly sensitive, state-of-the-art molecular biology technique for detecting viral extraneous agents, unintentionally introduced, unwanted, or foreign viruses also referred to as adventitious viruses, in biological products. These include vaccines, recombinant proteins, viral vectors used in gene therapy, and cell-based preparations for cell therapy.  

A key advantage highlighted in the chapter is the ability of NGS to detect a broad spectrum of viruses, including both known and unknown agents, within a single assay. By enabling NGS as an alternative to traditional invivo tests, the chapter also supports the 3R (reduce, replace, refine) principles and improved animal welfare. Regulatory agencies such as the EMA and the FDA already encourage 3R‑aligned testing strategies, reinforcing the role of NGS as an increasingly important tool for biotherapeutic development.2,3 

Bioinformatic Expectations and Validation Standards for NGS Workflows in Biopharma 

Beyond the wet lab, the new chapter places clear emphasis on bioinformatics as a critical component of NGS-based adventitious agent detection. It outlines a general NGS data analysis workflow, spanning initial raw read processing, quality filtration, and, when applicable, de novo assembly, followed by mapping against reference viral databases and scientific evaluation of results. 

To ensure reproducibility and comparability, the chapter requires transparent documentation of the complete bioinformatics pipeline. This includes software tools and versions, parameter settings, database sources, acceptance criteria for distinguishing true from false viral hits, and all the methods used for NGS analysis. Appropriate controls must be incorporated across the workflow, from sample preparation through reporting.

In addition, the chapter defines stringent validation expectations for NGS pipelines used as qualitative limit tests. This includes demonstrating specificity across a wide range of viruses, establishing the limit of detection (LOD) using suitable spiking materials, and ensuring the suitability of reference databases through well-annotated and diverse viral sequences. The guidance also specifies a two-step identification process, combining primary screening against a viral database with a counter screen, to remove false positives and confirm the validity of detected hits. Importantly, any change to software tools, versions, databases, or analysis parameters requires qualification or re-validation. 

Still Wondering How to Get Started with NGS?  

Turning Guidelines into Reproducible, Validated NGS Workflows 

Despite the new general chapter of the European Pharmacopoeia, implementing NGS to ensure therapeutic product quality and safety remains complex. Different classes of biological therapies require distinct sample preparation methodologies, and different sequencing platforms often demand highly specialized, tailored analysis pipelines.  

To help biopharma organizations navigate this complexity, the Ph. Eur. outlines the main steps of an NGS workflow based on the type of biological material used in R&D and manufacturing. The chapter provides detailed guidance on sample pretreatment steps, ranging from nuclease digestion to filtration, followed by nucleic acid extraction, post-extraction processing, and library preparation for both short and long-read sequencing. It also describes subsequent steps, the bioinformatics workflow from raw read quality control through reporting, and the scientific evaluation of results, including any required follow-up investigations.

The Challenge: Right Software Infrastructure 

For teams without deep NGS or bioinformatics expertise, translating these guidelines into practical, operational workflows remains challenging. Importantly, organizations preparing submissions for regulatory authorities must validate the entire NGS workflow end-to-end, including not only the wet laboratory steps but also the digital systems used for data processing, analysis, and reporting.  

Without a robust, validated software infrastructure, biopharma organizations struggle to implement compliant NGS pipelines. The guidelines require consistent parameter settings, proper database selection, and detailed version control of all tools, programs, and reference sequences. Fragmented or custom bioinformatics processes make it difficult to manage updates, revalidate pipelines, and ensure reproducibility over time, increasing the risk of non‑compliance as tools and databases, or workflows inevitably evolve.  

In addition, without centralized software to standardize analysis across short‑read, long‑read, targeted, and non‑targeted workflows, teams may generate inconsistent results that cannot withstand regulatory scrutiny for specificity (breadth of virus detection) or limit‑of‑detection validation. While outsourcing NGS data analysis may appear attractive initially, it often introduces long turnaround times, limited transparency, intellectual property risks, and high per-sample costs, challenges that become increasingly problematic as NGS testing scales across programs.  

By bringing NGS in-house with Genedata Selector, leading biopharma companies can combine the assurance of a trusted, off-the-shelf software solution with the scalability, control, and transparency required to operationalize validated NGS workflows across development and manufacturing.

Eliminate the Complexity of NGS with Genedata Selector 

Extracting and reporting accurate, decision-ready insights from NGS data is the most critical step of the workflow. Without reliable, reproducible analysis, the results of even the most rigorous sample preparation and sequencing cannot be fully trusted. Whether organizations are new to NGS, looking to scale and standardize existing workflows, or preparing regulatory submissions, Genedata Selector provides a clear path forward aligned with the requirements of the new European Pharmacopoeia Chapter 2.6.41 (Figure 1).   

Figure 1. Mapping how Selector, Genedata's NGS Analysis software supports biopharma compliance with European Pharmacopoeia guidelines
Figure 1. Mapping how Selector, Genedata's NGS Analysis software supports biopharma compliance with European Pharmacopoeia guidelines

Designed for agile and innovative biopharma and biotech organizations, Genedata Selector delivers accurate, streamlined NGS-based quality control. The software supports the enforcement of compliant workflows to ensure virus safety and identification of potential contamination across a broad range of biological modalities.  

Genedata Selector enables teams to process and manage NGS data in-house across any sequencing platform, standardize analysis pipelines, and make validated workflows available to scientists across functions — without requiring extensive bioinformatics expertise. For regulatory submissions, the software’s GxP-ready capabilities support compliance through end-to-end traceability, auditability, and protection of proprietary sequences and NGS data. By reducing operational complexity and regulatory risk, Genedata Selector simplifies compliance within the framework of Ph. Eur.2.6.41.

Unlock the Full Potential of NGS Across R&D and Manufacturing

NGS is rapidly becoming a central to biotherapeutic quality control, moving beyond a “nice-to-have” toward broader adoption across development and manufacturing. Using an end-to-end solution such as Genedata Selector for NGS data management, data processing, analysis, and reporting enables organizations to fully harness the potential of NGS across research, development, and manufacturing while meeting regulatory expectations.

By supporting validation ready, standardized, and reproducible NGS workflows, Genedata Selector helps biopharma organizations translate regulatory guidance into practical implementation. The result? Greater confidence in NGS-based quality control and the ability to deliver safe, effective therapies to patients faster and more cost-effectively. 

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References

1. European Directorate for the Quality of Medicines & HealthCare (EDQM). EPC adopts a cutting-edge HTS chapter to enhance viral contaminant detection in biological products. 2025. www.edqm.eu/en/-/epc-adopts-cutting-edge-hts-chapter-to-enhance-viral-contaminant-detection-in-biological-products

2. European Medicines Agency (EMA). Guideline on Principles for the Regulatory Acceptance of 3Rs (Replacement, Reduction, Refinement) Testing Approaches. 2016. www.ema.europa.eu/en/documents/scientific-guideline/guideline-principles-regulatory-acceptance-3rs-replacement-reduction-refinement-testing-approaches_en.pdf

3. U.S. Food and Drug Administration (FDA). Implementing Alternative Methods. 2026.

4. www.fda.gov/science-research/advancing-alternative-methods-fda/implementing-alternative-methods

FAQs

European Pharmacopoeia Chapter 2.6.41 outlines expectations for using NGS approaches in adventitious viral detection, with an emphasis on end‑to‑end control, validation, and reproducibility. Key elements include:

  • A complete, end‑to‑end NGS workflow, spanning sample preparation, sequencing, bioinformatics, and reporting
  • Broad viral detection capable of identifying both known and unknown viruses
  • Generic method validation to demonstrate fit-for-intended use, based on specificity and limit of detection
  • Product‑specific validation using appropriate controls and defined performance criteria
  • Routine assay controls to verify ongoing performance and detect contamination
  • Validated bioinformatics pipelines to support accurate data interpretation 

For Further details, refer to European Pharmacopoeia Chapter 2.6.41.

The chapter places significant emphasis on bioinformatics as a core component of NGS‑based viral detection. Required capabilities include: 

  • Quality control of raw sequencing reads, including de-multiplexing, trimming, and removal of low-quality bases
  • Primary viral screening through mapping against a broad, well-annotated reference database (for example, RVDB) to detect known and unknown viruses
  • Secondary confirmation of viral hits (counter-screening) using independent nucleotide databases (such as NCBI nr/nt) to reduce false positives and support follow-up analysis
  • Validated analysis pipelines with defined parameters, version control, and re-validation whenever tools, software, or databases change
  • Reference database suitability, ensuring completeness, accurate annotation, and minimal low-complexity content to prevent misalignment or misannotation
  • Structured, reproducible reporting that documents pipeline steps, software versions, databases, alignment criteria, and interpretation rules
  • Predefined interpretation criteria to distinguish true positives from false positives based on metrics such as read counts, genome coverage, and sequencing depth 

End-to-end NGS analysis software is critical because Ph. Eur. 2.6.41 emphasizes a fully integrated and validated workflow spanning sample processing, sequencing, bioinformatics, controls, reporting, and interpretation. A unified software environment is necessary to maintain traceability, version control, data integrity, and reproducibility across all workflow stages, supporting regulatory-ready viral safety testing and confident decision-making.

Validating NGS workflows for viral detection presents several challenges, including: 

  • Demonstrating broad sensitivity and specificity across diverse virus families, including known and unknown viruses, within different sample types and matrices  
  • Access to well-characterized spiking materials, such as  WHO reference panels, for assay validation  
  • Managing cross-contamination risks across workflow steps, including sample preparation, library preparation, and sequencing, which requires appropriate segregation of areas in the wet lab, barcoding strategies, and appropriate controls  
  • Validating complex bioinformatics pipelines, encompassing quality control, viral screening, counter-screening, database suitability, reproducibility, and re-validation following any software or database changes 

Managing NGS workflows in-house offers several advantages, including: 

  • Greater control and traceability across the complete end-to-end NGS workflow described in Ph. Eur. 2.6.41, from sample preparation through sequencing and bioinformatics  
  • Faster validation and re-validation cycles, as modular validation and rechecking are required whenever workflows or software components change 
  • Improved contamination control through direct oversight of segregation, barcoding strategies, and assay controls across all workflow steps 

Genedata Selector aligns with the expectations of Ph. Eur. 2.6.41 by providing an integrated, controlled environment that reflects the chapter’s end-to-end approach for NGS-based viral detection. Specifically, it supports alignment by enabling: 

  • End-to-end bioinformatics workflow continuity, covering data management, analysis, reporting, and follow-up actions in line with the chapter.  
  • Validation-ready bioinformatics pipelines, including quality filtering, primary viral screening, counter-screening to reduce false positives, database suitability management, version control, and structured reporting. 
  • Modular validation approaches through configurable Playbooks, allowing biopharma organizations to validate tailored to internal NGS assays. Genedata Selector can be validated as needed, after which teams can select and validate specific Playbooks. All Playbooks run on the same validated platform, reducing the effort required for validation and re-validation.  

Together, these capabilities help ensure that NGS workflows address the chapter’s expectations for sensitivity, specificity, reproducibility, and regulatory-ready documentation.