Jump to content

Validating Next-Generation Sequencing Assays in Light of Regulatory Changes

April 22, 2024
Urszula Cendrowska

Biopharmaceutical organizations are increasingly interested in integrating their next-generation sequencing (NGS) assays into a validated (GMP) environment. These assays are crucial for assessing the Critical Quality Attributes (CQAs) of biotherapeutics, particularly gene and cell therapy products. The potential of the NGS technique is increasingly recognized by biopharmaceutical companies and regulatory agencies.  As a result, a growing number of guidelines for biopharmaceutical companies have been published by regulatory authorities in recent years. These guidelines have progressively advocated for the adoption of NGS as a replacement for in vivo assays and as a supplement for various in vitro assays. Moreover, regulators specifically request NGS-based characterization for the commercial approval of advanced therapies.1  Genedata Selector® is an end-to-end platform for NGS data management and analysis that provides out-of-the-box GMP-required functionalities and enables biopharmaceutical organizations to perform various NGS-based assays in-house. Genedata is committed to supporting biopharma in its mission to improve the time to market of life-saving drugs. We empower companies to transition their workflows to a validated environment, not only by providing digital tools but also by facilitating community building and knowledge exchange among experts in the field.

Genedata Selector hosts regular industry workshops and Open Forums, where experts can interact, discuss their projects, and gain insights from their peers. Following a series of successful virtual industry workshops, Genedata Selector hosted the 9th Open Forum, the first in-person edition of this series of industry events. At the event, discussions were centered on the GMP-compliant NGS-based assays used for product characterization and safety assessment of cell and gene therapies.

Experts from 10+ leading biopharmaceutical companies in the Boston area, including AbbVie, Astellas, AstraZeneca, BMS, Regeneron, and Takeda, gathered in Lexington, Massachusetts to attend the event and exchange experiences. The event started with a warm welcome from Thomas Hartsch, Head of Business of Genedata Selector. His introduction began with a brief history of the Open Forum events, highlighting their continuous evolution and significance. He then referred to the revised ICH Q5A (R2) guidelines, which will come into effect on June 14, 2024. In the updated version of the guidelines, regulatory authorities have emphasized replacing traditional in vivo assays with NGS-based methods. This highlights the growing need to introduce NGS into regulated environments and the need for tools that enable a compliant analysis and management of the data generated by this technique.

The next speaker, Tracie Fradet, Associate Director, Cytogenomics from Astellas Institute for Regenerative Medicine (AIRM), shared the motivations of the Cytogenomics Group at AIRM to implement NGS in-house in a validated environment. Their goal is to develop expertise in evaluating the genetic stability of cell banks and drug substances. Their primary goal is to replace traditional in vitro and in vivo assays with NGS workflows. Tracie spoke about their productive collaboration with Genedata Selector, comparing it to a jigsaw puzzle where all pieces fell into place perfectly within a few months. She highlighted the platform’s ability to integrate, analyze, and share project-related data in a GMP environment for improved decision-making and faster time to market.

The event continued with another perspective on enabling NGS in the GMP environment. This was presented by Ludwig Macko, Head of Development of Genedata Selector. He explained why Genedata Selector is being recognized by leading biopharma companies. The platform is more often identified as a supporting partner in their mission to deliver safe treatments to patients in a timely manner. Ludwig gave an overview of the applications of Genedata Selector across modalities and stages of development. He explained the concept of Playbooks, wizard-based workflows, that are a key part of the platform. Playbooks simplify and automate the analysis, management, and report generation of NGS data. He highlighted the built-in capabilities of Genedata Selector that allow the platform to operate in a validated environment and support the transfer of the NGS assays to a GMP environment for any biopharmaceutical organization.

After a networking coffee break, the event shifted focus with the presentation by Krishnamurthy Shankarling, Principal Scientist at Bristol Myers Squibb. The talk focused on showcasing the Genedata Selector Playbooks in omics data management and analysis workflows. Krishnamurthy discussed the parameters needed to characterize AAV for gene therapy and presented how both short- and long-read sequencing technologies are used in the comprehensive development of AAV characterization workflows. He highlighted the ease and efficiency of using Genedata Selector Playbooks, which play a significant role in streamlining workflows to characterize AAV-based gene therapy, and their strong position to continue supporting such analyses in the future.

Genedata Selector Open Forum events provide participants with an open platform for knowledge exchange regarding the use of NGS in biopharmaceutical organizations.

The event also provided a preview of the Genedata Selector platform with a presentation and an interactive demo given by Devon Ryan, Head of Scientific Consulting at Genedata Selector. He demonstrated the lifecycle of a typical NGS-based assay, showcasing the pivotal role of Genedata Selector Playbooks in supporting this process. He started his talk with the initial phase of the lifecycle in the wet lab, where various tests are performed to determine the optimal experimental conditions for the NGS library preparation kits. He then explained the next step, where NGS data is tracked and analyzed within the platform. At this stage, Playbooks support the user journey from data transfer, through analysis and visualizations of results, to report generation. They also enable faster and better-informed decision-making by providing clear go/no-go signals at the end of the analysis. Devon concluded his talk by highlighting the role of Playbooks in enabling the use of NGS in a validated environment that complies with industry standards and regulatory requirements.

The last presentation was given by Aurora Signorazzi, Scientist & Project Leader at J&J. Aurora shared how her team leverages Genedata Selector to deploy NGS for the detection of adventitious viruses and quality testing of the products, as required by the regulatory authorities. Aurora presented a case study illustrating their biosafety assays to detect bacteria, viruses, and mycoplasma, which are typically challenging to detect with traditional methods. She demonstrated their application of Genedata Selector for automated and fast data analysis with intuitive go/no-go signals, based on pre-established rules. The results of the exemplary spike-in experiment were summarized in a straightforward table with the results based on the analysis outcome. She emphasized that unlike in vitro assays, NGS is an agnostic technique able to identify various contaminants accurately.

Each presentation was followed by an engaging Q&A session, where all attendees were invited to ask questions or comment on the presentations. This session sparked stimulating discussions and provided an excellent opportunity to gain further insights into the projects presented.

After the first part of the meeting, the event transitioned to a more interactive stage, starting with the poster session. This provided participants with an additional networking opportunity and a chance to familiarize themselves with the selected use cases of Genedata Selector. The poster session provided a valuable opportunity for attendees to deepen their understanding of the specific applications of the Genedata Selector, such as:

  1. Next-Generation Sequencing-Based Biosafety Assessment of Biologics
  2. Advancing Cell Therapies Using NGS as a Multi-Attribute Method
  3. NGS-Based Quality and Safety Control for Cell and Gene Therapy Products
  4. Revolutionizing Computerized System Validation for NGS-Based Assays
  5. Streamlining NGS-Based Workflows in Cell Line Development

The poster session was followed by a panel discussion featuring Ludwig Macko, Krishnamurthy Shankarling, and two special guests – Lianchun Fan, Director of Cellular & Molecular Biology Science at Abbvie, and Athea Vichas, Senior Scientist at Bristol Myers Squibb.  

The panelists shared their perspectives on leveraging NGS to streamline product characterization and safety. Lianchun briefly summarized the ICH Q5 (R2) process in which he was involved. He acknowledged that the process was meticulous and lengthy, with many stakeholders and rounds of revisions involved. The discussion then focused on assay standardization and simplifying workflows. The panelists highlighted that despite the increasing number of papers on NGS-based methods, it is critical to maintain knowledge exchange across organizations. Athea mentioned that Genedata played an essential role in introducing and driving the knowledge transfer between gene therapy and cell therapy groups. Both groups can leverage the Playbook developments and the knowledge accumulated independently to drive their R&D. She also emphasized the multi-attribute method (MAM) potential of NGS that her group is currently exploring. The panelists also touched on batch-to-batch comparisons with NGS. Overall, the panel was highly interactive, with all attendees of the Open Forum given the chance to contribute to the discussion by participating in digital polls and asking questions of the panelists. The poll results provided valuable insights into the applications of NGS across the participating organizations. As expected, most voters indicated that NGS standardization and assay validation processes are the most applied for wet lab and NGS core functions. Furthermore, the polls revealed that most of the participating organizations are considering applying NGS assays for adventitious agent detection and monitoring plasmid/host cell contamination. These results highlight the potential of NGS technology in the biosafety evaluation of advanced therapy medicinal products (ATMPs) and explain the recent increase in recommending NGS-based assays by the regulatory guidelines.

The event concluded with a workshop focused on the NGS-driven Critical Quality Attributes (CQAs) assessment. Open Forum attendees were encouraged to network, share knowledge, and engage in ongoing scientific discussions. Additionally, all attendees were able to participate in the tailored Genedata Selector demo sessions focusing on the core applications of the platform for cell and gene therapy products manufacturing and development, including:

  1. Comprehensive NGS-Based Adventitious Agent Detection for Cell and Gene Therapy Products. This demo showcased a use case for AAV production and long-read assays using Playbooks in Genedata Selector for the automation of adventitious agent detection and critical quality attributes assessment. The demo concluded with the generation of go/no-go results using the platform for quality control checks such as plasmid contamination and AAV fusion detection.
  2. NGS as a Multi-Attribute Method for Cell Therapy Production QC. This demo presented a case study of how Genedata Selector supported the analysis of data obtained from the Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB in Stuttgart, Germany. It showed how the customized and standardized Playbooks were used to assess several CQAs of cell therapy products by using NGS as a multi-attribute method (MAM).
  3. NGS as a Multi-Attribute Method to Support AAV Gene Therapy Production and Characterization. This demo showed how Genedata Selector supports AAV gene therapy production and critical quality attribute assessment using NGS as the multi-attribute method. It showcased how the platform enables assessment of the sequence integrity, plasmid contamination, and adventitious agent detection in one assay.

The opportunity to repeat the demonstrations is still available and demo sessions can be conveniently arranged to suit the availability of the requester.

Request Demo

Overall, the 9th Genedata Selector Open Forum was a success, providing attendees with an open platform for interesting talks and insightful knowledge exchange regarding the use of NGS for ATMP development and manufacturing. The in-person format allowed face-to-face interactions, which are crucial for community building. Attendees appreciated the collaborative environment to discuss the best practices and the high engagement in the networking and interactive sessions showed a need for such an open platform. Genedata Selector is proud to provide an open platform for scientific discussions with our industry workshops that have increasingly captured the interest of the growing community of leading biopharmaceutical organizations. The meetings are typically themed, with a central focus on NGS-based assays. Register today to become a part of our unique community and stay informed about all upcoming meetings so you don’t miss out on any opportunities!

Register Your Interest

  1. Committee for Medicinal Products for Human Use (CHMP) and Committee for Advanced Therapies (CAT), European Medicines Agency (EMA) Zolgensma Assessment Report (2020).