Comprehensive genomic profiling (CGP) describes technologies that allow profiling of all major types of genomic alterations, including simple nucleotide variation (SNV and indel), somatic copy number alteration (SCNA), structural variation (SV), and aggregate markers of genome damage such as Tumour Mutation Burden (TMB) and microsatellite instability (MSI). CGP could lead to improved access to molecularly targeted therapies for cancer patients but, aside from a few accredited commercial and academic providers, is not widely used in routine pathology practice. Aspects of CGP presenting barriers to broad adoption include cost, technical complexity, lack of reimbursement, and a perceived lack of clinical utility. Here we summarise the experience of Peter Mac’s Pathology Department in providing CGP in the translation research setting over three years of testing for personalised medicine trials. We find that characterising tumours using a comprehensive in-house clinical research panel provides useful diagnostic and predictive information that impacts patient care in a number of cases however at relatively high per sample cost. In comparison, we describe our experience with one of the first kit-based CGP research products on the Australian market meeting the requirements for routine CGP.
All authors contributed equally to this body of work