Patients suspected of having a rare genetic disease often experience lengthy and costly diagnostic odysseys. The timing of whole exome sequencing (WES) in the testing sequence, its diagnostic yield and test costs in the sequence all factor into estimates of cost-effectiveness analysis for health technology assessment.

We modeled the diagnostic pathway using a discrete event simulation model, starting with the first test result. We defined and populated the simulation based on data from the electronic medical records of n=307 from the Care-for-Rare SOLVE multi-center Canadian observational cohort. Five alternative diagnostic pathways were modeled based on the observed data: no WES, and WES as the first, second, third or fourth test in the sequence. WES as the second test in the sequence is considered standard of care in medical genetic centers in Canada. We assessed effectiveness of WES in terms of diagnostic yield, time to diagnosis, and costs as patient-level overall test costs (2020 CAD/USD) across the diagnostic pathway.

Compared to molecular and specialized diagnostic tests only (i.e., no WES), WES increased diagnostic yield from 5 percent to 40 percent. The shortest time to diagnosis for those with a diagnosis was 1.82 years in the diagnostic pathway with WES as the second test. Test costs for each pathway were CAD2,800 (USD2,087, no WES), CAD2,700 (USD2,013, WES as first test), CAD3,500 (USD2,609, WES as second test), CAD4,500 (USD3,354, WES as third test), and CAD5,300 (USD3,951, WES as fourth test).

Placing WES earlier in the diagnostic pathway for patients suspected of having a rare disease is associated with an increased diagnostic yield, reduced time to diagnosis and lower overall test costs with the benefits being greater the earlier in the pathway that WES is implemented.