Cellular pathology and molecular diagnostics for cancer

Recent developments in knowledge of cancer at the molecular level have led to a growing demand for tissue-based predictive analysis to inform therapeutic decision-making. Molecular parameters are also being increasingly incorporated into traditionally morphology-based diagnostic and prognostic classification systems. The resulting broader application of molecular techniques for interrogation of tissue samples requires adaptation of cellular pathology methods. A number of large-scale initiatives underway worldwide, including the Cancer Research UK Stratified Medicine Programme, are attempting to establish the evidence base and develop the teams, processes and infrastructure necessary to deliver this approach in routine practice.This thesis describes the findings of work in this area including collaborative efforts through the Stratified Medicine Programme and STRATFix consortium in the areas of patient consent, data, technology, tissue fixation and processing, utility of alternative tissue fixatives and pathologist or digital tumour content assessment. This work has demonstrated that acquisition of tissue surplus to diagnostic requirements for DNA-based tests is acceptable to patients, that targeted mainly ‘hotspot’ sequencing of up to five clinically relevant genes is feasible in a single tissue sample and that clinical data systems in their current form require a large amount of manual intervention to produce cancer data in a format compatible with the current NHS information standard. Furthermore, this research has demonstrated the variation in different aspects of tissue sample handling despite an increasing number of laboratories receiving accreditation to ISO standards, with its central focus on uniformity of process. There is also description of variation in tumour content assessment by a group of experienced pathologists using online whole slide imaging, indicating that accurate tumour quantification in samples submitted for sequencing is likely to require digital image analysis. This work shows that as a ‘molecular friendly’ fixative, the PAXgene® Tissue system provides tissue preservation generally suitable for morphological assessment and diagnosis, with the exception of lymphoid tissue for which further optimisation work is in progress. Histochemical techniques in use in our laboratory appear to be directly transferable to PAXgene® Tissue-fixed paraffin embedded tissue but immunohistochemistry requires protocol modification, particularly for antigens located in the cell nucleus. Double-stranded DNA yields from PAXgene® Tissue-fixed, paraffin embedded tissue are at least comparable to those obtained from matched formalin-fixed paraffin-embedded tissue and show better preservation with less DNA fragmentation.This body of work has enabled me to develop knowledge, skills and evidence to contribute to the crucial role of cellular pathology in the implementation of stratified cancer medicine for improved patient care