Industry Experiences in Bringing NGS-Based Biosafety and Quality Control Workflows In-House
September 29, 2025
Alison Waterfield
The development of biologics and advanced therapies increasingly depends on robust biosafety testing strategies that can keep pace with evolving regulatory expectations. As next-generation sequencing (NGS) technologies gain traction as unbiased, highly sensitive tools for detecting adventitious agents, biopharmaceutical organizations are moving toward in-house solutions that offer greater control, scalability, and data integrity.
Recent updates to regulatory guidelines — including ICH Q5A(R2), USP 1042, and EDQM 2.6.41 — reflect a growing acceptance of NGS-based assays as replacements for traditional in vivo methods. These changes are driving the need for digital platforms that support end-to-end NGS workflows, from assay development to data analysis and interpretation, in preparation for deployment in validated environments.
Genedata Selector is committed to supporting this transition by providing software solutions that streamline NGS workflows and facilitate regulatory alignment. Through its Open Forum series, Genedata brings together experts from across the industry to share insights, exchange best practices, and accelerate the adoption of in-house NGS for biosafety testing.
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Recap of the 11th Genedata Selector Open Forum on In-House NGS Workflows in Biopharma Industry
On September 23, 2025, Genedata Selector hosted its 11th Open Forum Industry Workshop, bringing together experts from over 40 leading biopharma organizations. The virtual live event focused on the adoption of in-house NGS-based workflows for biosafety testing and quality control, and how organizations are designing, automating, and scaling up these workflows in the context of evolving regulatory expectations.
During a warm welcome to the event, Thomas Hartsch, Head of Genedata Selector, emphasized the growing importance of bringing NGS workflows in-house, particularly in early process development and cell line characterization. He highlighted how recent updates to ICH Q5A(R2), USP 1042, and EDQM 2.6.41 are accelerating the shift away from traditional in vivo testing toward non-targeted sequencing approaches. These changes are prompting biopharma organizations to invest in digital platforms that support data integrity, scalability, and readiness for regulatory compliance.
AbbVie’s Approach to In-House NGS-Based Adventitious Virus Detection for Biosafety Testing
Sakthi Balaji, Senior Scientist II at AbbVie, shared her team’s approach to developing an in-house adventitious virus detection assay using high-throughput sequencing. She outlined the advantages of NGS over traditional in vivo and in vitro methods, including broader detection capabilities, faster turnaround times, and alignment with the 3R principles. Sakthi presented study results evaluating extraction kits, cDNA synthesis, and library preparation workflows using viral nucleic acid mixes and inactivated viruses. She also discussed sensitivity testing across varying cell concentrations and the use of Genedata Selector for automated analysis. Sakthi concluded by highlighting next steps toward assay validation, including reproducibility testing and threshold setting using WHO reference panels.
Automating GMP-Ready NGS Workflows for Adventitious Agent Detection with Genedata Selector
Michael Johnson, Scientific Account Manager at Genedata, demonstrated how Genedata Selector automates NGS-based adventitious agent detection (AAD) workflows for GMP and lot release. He outlined key bioinformatics steps such as host cell sequence subtraction, viral database selection, and result interpretation. Michael showed how Genedata Selector’s guided interface streamlines sample registration, data processing, and report generation, while built-in compliance features support FDA 21 CFR Part 11 requirements. He also highlighted customizable Playbooks and dashboards that simplify deployment in GxP environments. Michael concluded by sharing a roadmap for validation and implementation, showing how Genedata Selector enables consistent, reliable results without requiring expert bioinformatics knowledge. The opportunity to repeat the demonstration is still available:
Fujifilm Diosynth Cuts Bioreactor Contamination Detection Time from 7 Days to Under 24 Hours Using Genedata Selector
Andrew Hillhouse, Principal Scientist at Fujifilm Diosynth Biotechnologies, presented a case study on using Oxford Nanopore sequencing for rapid bioreactor contamination detection. His team achieved species-level identification in under 24 hours, significantly faster than the typical 7–11 day turnaround for outsourced testing. Using Genedata Selector’s automated Playbooks for base calling and microbial classification, they confidently identified Micrococcus luteus while keeping data in-house. Andrew emphasized Genedata Selector’s speed, accuracy, and built-in analysis capabilities, and discussed its broader value in supporting scalable, compliant workflows for adventitious agent detection. Andrew highlighted the importance of digital infrastructure in accelerating biosafety decision-making.
Panel Discussion
The second half of the Open Forum brought together all speakers for a live panel discussion moderated by Christoph Bredack, Business Account Manager at Genedata. The conversation focused on how biopharma organizations are adapting their virus safety strategies in response to the updated ICH Q5A(R2) guideline, and how in-house NGS workflows are being developed to meet emerging regulatory expectations.
Panelists shared real-world experiences with assay development, validation planning, and data analysis challenges. They discussed the complexity of interpreting NGS results, the importance of building trusted analysis pipelines, and strategies for avoiding false positives. The conversation also explored database selection, long-read sequencing use cases, and the role of AI and machine learning in enhancing virus detection and contamination control.
Ana from Johnson & Johnson shared her approach to validation, including detection breadth and establishing limits of detection. Sakthi described modular validation plans at Abbvie, while Michael emphasized the role of compliant software in supporting computerized system validation. Andrew reflected on his organization’s investment in NGS and the drivers behind the shift toward in-house workflows. All panelists agreed that regulatory clarity and digital infrastructure are key to future-proofing biosafety testing.
Event Summary: Industry Shift Toward In-House NGS Workflows and Insights from Live Q&A Sessions
Each presentation was followed by a lively and engaging Q&A session, buzzing with insightful questions from attendees. The speakers answered all questions live, making the event highly interactive and informative. In summary, the 11th Genedata Selector Open Forum highlighted the industry’s shift toward in-house NGS workflows for biosafety and quality control, and the importance of preparing these workflows to meet evolving regulatory expectations.
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