Partial Restriction. Restriction lift date: 2030-09-30
Establishment of Next Generation Sequencing (NGS) in a clinical diagnostic laboratory for diagnostic and research purposes
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Date
2025
Authors
Werner, Reiltin
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Journal ISSN
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Publisher
University College Cork
Published Version
Abstract
This thesis examines the implementation of Next Generation Sequencing (NGS) technology for cancer molecular profiling within a previously NGS-naïve clinical pathology laboratory at Cork University Hospital (CUH). The project addresses the growing clinical need for multi-gene analysis by moving from single-gene testing to a comprehensive NGS approach, significantly improving diagnostic capabilities and research integration. The thesis had three primary objectives:
1) Implementation of an Irish National Accreditation Board (INAB) accredited NGS diagnostic service to ISO 15189 standards in an NGS-naïve pathology department.
2) Expand NGS panel repertoire from tissue- to liquid-based and incorporate the platform into clinical research protocols.
3) Training and education of cancer centre staff and trainees in NGS.
Implementation of NGS in the Clinical Diagnostic Setting to ISO 15189 Standards: This involved optimising and validating targeted NGS panels for formalin-fixed paraffin-embedded (FFPE) tumour tissue and plasma samples, reducing the turnaround time (TAT) for results from three weeks to less than seven days. It also assessed the potential of novel automated NGS technologies capable of delivering results within 24 hours—an advancement not yet available in Ireland.
Expand NGS Panel Repertoire and Incorporate Research Protocols: This objective focused on expanding protocols for both tissue and liquid biopsies and conducting concordance studies, with an initial emphasis on non-small cell lung cancer (NSCLC). The research project described in Chapter 4 “Temporal Evaluation of Oncogenic Driver Mutations and Co-Variant Changes in NSCLC Patients Using NGS,” demonstrated the success of NGS in both tumour and plasma samples. It contributed significantly to understanding tumour evolution and treatment response. The attainment of accreditation to ISO 15189 standards for liquid biopsy enabled CUH to participate in pan-European studies and expand its NGS research output and collaborations.
Training and Education: A primary focus of the project was developing comprehensive NGS training programmes for medical scientists, doctors in training (DIT), and undergraduate and postgraduate students. These accreditation-compliant programmes have ensured that CUH has highly skilled professionals capable of using NGS technology in diagnostic and research contexts. The educational framework established supports the long-term development of NGS services at CUH and contributes to ongoing professional and academic advancement in pathology.
In conclusion, the project achieved and exceeded its key objectives. By establishing robust pathways for multidisciplinary collaboration and embedding NGS technology in clinical diagnostics, CUH has positioned itself as a molecular research hub. The success of the NSCLC study, highlights the clinical benefits of NGS and sets a solid foundation for future advancements in precision oncology. The project’s achievements in diagnostic accuracy, research output and professional development have put CUH at the forefront of molecular pathology, paving the way for further innovations and collaborations.
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Partial Restriction
Keywords
Next Generation Sequencing , Clinical diagnostic pathology , Molecular profiling
Citation
Werner, R. 2025. Establishment of Next Generation Sequencing (NGS) in a clinical diagnostic laboratory for diagnostic and research purposes. PhD Thesis, University College Cork.