Prospective comparison of the cost-effectiveness of clinical whole-exome sequencing with that of usual care overwhelmingly supports early use and reimbursement

Purpose: To undertake the first prospective cost-effectiveness study of whole-exome sequencing (WES) as an early, routine clinical test for infants with suspected monogenic disorders. Methods: Cost data for diagnosis-related investigations and assessments were collected for a prospective, sequential clinical cohort of infants (N = 40) who underwent singleton WES in parallel to usual diagnostic care. We determined costs per patient, costs per diagnosis, and incremental costs per additional diagnosis for three alternative strategies for integrating WES into the diagnostic trajectory. We performed a sensitivity analysis to examine the robustness of estimates and bootstrapping (500 replications) to examine their distributions. Results: Standard care achieved an average cost per diagnosis of AU$ 27,050 (US$ 21,099) compared with AU$ 5,047 (US$ 3,937) for singleton WES. If WES had been performed after exhaustive standard investigation, then there would have been an incremental cost per additional diagnosis of AU$ 8,112 (US$ 6,327). Using WES to replace some investigations decreases this incremental cost to AU$ 2,622 (US$ 2,045), whereas using it to replace most investigations results in a savings per additional diagnosis of AU$ 2,182 (US$ 1,702). Conclusion: Use of WES early in the diagnostic pathway more than triples the diagnostic rate for one-third the cost per diagnosis, providing strong support for reimbursement as a clinical test.