Authors' objectives: The primary objective of this report update is to estimate costs associated with CMA, whole exome sequencing (WES) and whole genome sequencing (WGS) (proband and trio) tests for a targeted patient population consisting of children with ASD from an institutional payer perspective over 5 years. The secondary objective is to compare the incremental costs and diagnostic yields of CMA, WES and WGS in hypothetical clinical testing scenarios in an exploratory cost-consequence analysis.

Authors' results and conclusions: The cost per ASD sample in Year 1 was $1960 (95% CI: 1899, 2020) for WES (HiSeq® 2500), $1981 (95% CI: 1909, 2054) for WES (NextSeq® 550), $3350 (95% CI: 3234, 3467) for WGS-proband (HiSeq X™) and $6556 (95% CI: 6278, 6832) for WGS-trio (HiSeq X™) compared to $825 (95% CI: 789, 859) for CMA. Reagent supply costs accounted for the largest proportion of costs for each type of test. The total institutional program cost to offer CMA for ASD diagnosis over five years was $1.16 million (95% CI: 1.11, 1.21) compared to $2.73 million (95% CI: 2.65, 2.82) for WES (HiSeq®2500), $2.79 million (95% CI: 2.69, 2.89) for WES (NextSeq® 550), $4.68 million (95% CI: 4.52, 4.85) for WGS-proband (HiSeq X™) and $27.78 million (95% CI: 26.59, 28.95) for WGS-trio (HiSeq X™) based on 300 ASD cases per year. A cost-consequence analysis revealed a cost of over $30,000 per additional patient with a positive finding if CMA were to be replaced by CMA plus WES or by WGS proband or trio. Additional research is required to assess the impact of CGES on the pathway of care for children with ASD and to measure ultimate improvements in health outcomes as a result of testing. This study provides comprehensive cost data for use in future economic evaluations of clinical genome and exome sequencing in ASD and allows for a costing model that can be easily adapted to other pediatric patient populations.

Authors' methods: Using a bottom-up microcosting approach, the opportunity cost per sample excluding mark-ups, fees and charges for CMA, for WES (on the Illumina HiSeq® 2500 and NextSeq® 550 platforms) and for WGS (probands and trios) on the Illumina HiSeq X™ platform for pediatric patients with ASD were estimated. This was done from an institutional payer perspective based on the diagnostic laboratory practices at The Hospital for Sick Children (SickKids), Canada. The cost per sample was determined for each year of a five-year program. Total program costs to service the ASD pediatric population were also estimated over five years. A probabilistic analysis (PA) was conducted to incorporate parameter uncertainty in the model.

Project Status: Completed

Year Published: 2019

URL for published report: https://lab.research.sickkids.ca/task/wp-content/uploads/sites/66/2019/02/Microcosting-REPORT-NO-2018-01_FINAL.pdf

English language abstract: An English language summary is available

Publication Type: Not Assigned

Country: Canada

Organisation Name: Technology Assessment at SickKids

Contact Address: Program of Child Health Evaluative Sciences, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8 tel: (416) 813-8519 fax: (416) 813-5979

Contact Name: wendy.ungar@sickkids.ca

Contact Email: wendy.ungar@sickkids.ca

Copyright: Technology Assessment Unit of the Hospital for Sick Children (TASK)