Clinical exome sequencing reports: current informatics practice and future opportunities

Abstract

The increased adoption of clinical whole exome sequencing (WES) has improved the diagnostic yield for patients with complex genetic conditions. However, the informatics practice for handling information contained in whole exome reports is still in its infancy, as evidenced by the lack of a common vocabulary within clinical sequencing reports generated across genetic laboratories. Genetic testing results are mostly transmitted using portable document format, which can make secondary analysis and data extraction challenging. This paper reviews a sample of clinical exome reports generated by Clinical Laboratory Improvement Amendments-certified genetic testing laboratories at tertiary-care facilities to assess and identify common data elements. Like structured radiology reports, which enable faster information retrieval and reuse, structuring genetic information within clinical WES reports would help facilitate integration of genetic information into electronic health records and enable retrospective research on the clinical utility of WES. We identify elements listed as mandatory according to practice guidelines but are currently missing from some of the clinical reports, which might help to organize the data when stored within structured databases. We also highlight elements, such as patient consent, that, although they do not appear within any of the current reports, may help in interpreting some of the information within the reports. Integrating genetic and clinical information would assist the adoption of personalized medicine for improved patient care and outcomes.

Keywords: Common data elements; Health Level-7 Fast Healthcare Interoperability Resources; clinical WES; electronic health records; exome report; structured vocabulary.

Figure 1.

A typical clinical exome sequencing workflow from patient first presenting symptoms at the clinic to care management based on the sequencing report.

Figure 2.

Process for identifying and validating common data elements (CDEs) from sample clinical exome reports.

Figure 3.

Major domains and subdomains identified by comparing the different clinical exome sequencing reports. Four major domains of information were identified within an exome sequencing report. The homogenous domains, Clinical Indication and Methods, each have elements only (not shown), whereas the heterogeneous domains, Clinical Order and Results, are subdivided into subdomains, each with their own elements (not shown).