Pharmacy Practice Faculty Publications

Title

Clinical Exome Sequencing Reports: Current Informatics Practice and Future Opportunities

Document Type

Article

Publication Date

5-23-2017

Journal Title

Journal of the American Medical Informatics Association : JAMIA

ISSN

1527-974X

DOI

10.1093/jamia/ocx048

PubMed ID

28535206

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