The recent release of powerful next-generation sequencing platforms, which can provide whole exome sequencing (WES) or whole genome sequencing (WGS) in quicker timelines and at reduced costs, has resulted in proposals for these diagnostic testing methods to be routinely integrated into clinical practice in multiple settings. However, the complexities of these diagnostic approaches, and the minimal comparative evidence available on them, creates difficulties in the evaluation of their diagnostic performance. Novel approaches need to be developed to improve the health technology assessment (HTA) of WES and WGS.

Several HTAs on genetic testing and the use of WES or WGS in fetal medicine were reviewed. Information on factors associated with this diagnostic modality that affect typical test accuracy assessment (e.g., sensitivity and specificity) was extracted. The multiple steps required for completing a WES or WGS test, and the potential for the introduction of errors (type I or type II) at each of these steps, were mapped and examples provided. The clinical and economic implications associated with imperfect and uncertain test accuracy were described.

Limited data on analytical and clinical validity were identified. WES and WGS are multistep processes and errors were found in sampling, molecular sequencing, bioinformatic filtering, and variant interpretation; therefore, the assumption that WES or WGS is 100 percent sensitive or specific is not reasonable. Although alternative evidence-based estimates are unlikely to be available, the inevitability of such errors, and their implications in terms of comparative effectiveness, safety, and cost effectiveness, should be described in HTAs.

While unknown diagnostic accuracy remains an issue with WES and WGS testing, formal sensitivity analysis of test performance characteristics should be conducted as part of HTAs. A checklist has been developed to assist those involved in HTA and policy to understand the potential for inaccurate test results in clinical practice, and the risk-benefit implications of these diagnostic errors for patients.