Implementing whole genome and transcriptome sequencing for cancer patients in routine healthcare: a comprehensive guide to costing

BACKGROUND: Molecular characterisation of solid tumours contributes to a precise diagnosis and can uncover a range of drug targets and biomarkers, improving patient management. Whole genome sequencing (WGS) combined with whole transcriptome sequencing (WTS) is the most comprehensive approach in molecular cancer diagnostics and is therefore becoming increasingly integrated in clinical care. A critical challenge in implementing WGS/WTS as a clinical-grade test is its high cost compared to targeted sequencing approaches, prohibiting wider use and access. METHODS: To dissect this limitation, we performed a micro-costing analysis of an established WGS/WTS workflow based on short-read sequencing technology. We categorised the costs as follows: consumables, equipment and maintenance, personnel, and data processing/storage. We considered various scenarios, including sample volumes, personnel and equipment redundancy, inflation and mean coverage. RESULTS: We have developed a multidimensional costing model that identified consumable costs, particularly flow cells, as the main cost drivers. While personnel and equipment costs decreased with larger case volumes processed (scaling effects), consumable and data processing/storage costs did not change significantly. CONCLUSIONS: Thus, falling prices of consumables would facilitate the broad implementation of WGS/WTS as a clinical-grade test.