Strategies to achieve 'real-time' reporting from clinical cancer panels

A Fellowes, R Vedururu, K Doig, E Thompson, G Ryland, G Reid, D Choong, H Xu, A Bell and S Fox

Pathology Dept, Peter MacCallum Cancer Centre, Parkville, Melbourne

Next generation sequencing (NGS) methods have revolutionised the clinical diagnosis of cancer from tissue specimens and enabled an era of personalised medicine that has improved clinical outcomes for many cancer patients. As approved treatment options and clinical trials for novel personalised therapies become more accessible, there is an incentive to perform larger scale clinical sequencing, up to and including whole genome sequencing (WGS). Conversely, the volume of data generated by NGS technologies creates a tension in the clinical laboratory, where turnaround time remains an important determinant of success for genomic-based prescribing. Therefore, amongst the goals of the Cancer 2015 project, a Victoria-based longitudinal pan-cancer study now in its fifth year, one is to drive the development of technologies needed for real-time implementation of NGS technology in the somatic disease context. Three strategies will be discussed: 1) use of targeted gene panels with high clinical utility; 2) harnessing automation and electronic workflow management systems, and 3) development of a variant management and reporting database, PathOS, to store, associate and re-use variant annotations, evidence and report comments across a range of clinical scenarios.