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AIMS New sequencing technologies allow increased opportunities to use genomic-based diagnostic tests (genomic tests) in routine clinical practice, which will impact healthcare budgets and patients' outcomes. This article aims to generate a list of recommendations on how the principles and methods of cost-effectiveness analysis (CEA) can be used to quantify the costs and benefits of genomic tests. METHODS A systematic literature search identified publications describing the use of CEA to evaluate genomic tests. Data were extracted as key concepts to produce a thematic list of previously described challenges and solutions to using CEA to evaluate genomic tests. Defining features of evaluating genomic tests were categorized into a list of key recommendations for applying methods in practice and for research needs. RESULTS Features producing challenges in the implementation of CEA to evaluate genomic tests were as follows: the ability of the tests to diagnose multiple disorders; potential consequences for future generations suggesting an infinite time horizon; and the potential need to consider nonhealth benefits. CONCLUSIONS CEA was identified as an appropriate evaluative framework for genomic tests, although standard methods may need modification and important method research questions remain. Key recommendations suggest a need for research to reflect: sharing genomic information across generations; genomic tests for multiple disorders; and health and nonhealth benefits.