Whole exome sequencing in molecular diagnostics of cancer decreases over time: evidence from a cost analysis in the French setting

Objectives Although high-throughput sequencing is revolutionising medicine, data on the actual cost of whole exome sequencing (WES) applications are needed. We aimed at assessing the cost of WES at a French cancer institute in 2015 and 2018. Methods Actual costs of WES application in oncology research were determined using both micro-costing and gross-costing for the years 2015 and 2018, before and after the acquisition of a new sequencer. The entire workflow process of a WES test was tracked, and the number and unit price of each resource were identified at the most detailed level, from library preparation to bioinformatics analyses. In addition, we conducted an ad hoc analysis of the bioinformatics storage costs of data issued from WES analyses. Results The cost of WES has decreased substantially, from euro1921 per sample (i.e. cost of euro3842 per patient) in 2015 to euro804 per sample (i.e. cost of euro1,608 per patient) in 2018, representing a decrease of 58%. In the meantime, the cost of bioinformatics storage has increased from euro19,836 to euro200,711. Conclusion This study suggests that WES cost has decreased significantly in recent years. WES has become affordable, even though clinical utility and efficiency still need to be confirmed.

Automated summary

The study assessed the actual costs of whole exome sequencing (WES) at a French cancer institute in 2015 and 2018, finding a substantial decrease in cost from 1921 euros per sample in 2015 to 804 euros per sample in 2018. Despite the decrease in WES cost, bioinformatics storage costs have increased significantly over the same period.