Targeted Next Generation Sequencing to improve solid tumour diagnosis using tissue-derived and cell-free DNA

  • Lauren McConnell

Student thesis: Doctoral ThesisDoctor of Philosophy


Next generation sequencing (NGS) allows for high throughput sequencing of DNA and is commonly utilised in oncology research. Whilst whole genome and exome sequencing have been used to identify novel mutations in cancer patients, a more rapid and cost-efficient technology is required for clinical practice. Targeted NGS allows for specific regions of interest in the genome to be enriched and sequenced enabling deeper coverage. Targeted NGS has applications in disease diagnosis, monitoring response and/or resistance to treatment and early detection of disease recurrence. It has become an attractive research tool and targeted gene panels have been approved by the Food and Drug Administration (FDA) for use in the clinical setting. The purpose of this thesis was to investigate the use of targeted NGS in improving diagnosis in sarcoma and monitoring response to treatment in breast and lung cancer patients, using DNA extracted from tissue or circulating tumour-derived DNA (ctDNA) from plasma. ctDNA is highly fragmented DNA released into the bloodstream from tumour tissue and is a common analyte for liquid biopsy in both the research and clinical setting. There is little literature surrounding the use of targeted NGS and ctDNA in sarcoma, most likely due to a lack of suitable NGS panels for fusion gene analysis. For this study, a sarcoma-specific gene panel was designed, optimised and validated using DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue to improve diagnosis in fusion-positive sarcoma patients. The gene panel was then evaluated using cell-free DNA (cfDNA) from a small cohort of sarcoma patients with matched tissue available to assess the feasibility of using ctDNA for diagnostic use. To assess the value of ctDNA in monitoring response to treatment, two pilot studies were carried out in cancers more prevalent than sarcoma: breast and lung cancer. This thesis investigates response to neoadjuvant chemotherapy (NACT) in breast cancer patients and radiotherapy in non-small cell lung cancer (NSCLC) patients, using targeted sequencing mutation analysis on ctDNA. In summary, the use of targeted NGS using both tissue and plasma-derived DNA has been evaluated in a range of cancer types to investigate its use in cancer diagnosis and disease monitoring.
Date of AwardJul 2020
Original languageEnglish
Awarding Institution
  • Queen's University Belfast
SupervisorDavid Gonzalez de Castro (Supervisor) & Manuel Salto-Tellez (Supervisor)

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