Journal:Information technology support for clinical genetic testing within an academic medical center

Full article title	Information technology support for clinical genetic testing within an academic medical center
Journal	Journal of Personalized Medicine
Author(s)	Aronson, Samuel; Mahanta, Lisa; Ros, Lei L.; Clark, Eugene; Babb, Lawrence; Oates, Michael; Rehm, Heidi; Lebo, Matthew
Author affiliation(s)	Partners HealthCare, Brigham & Women’s Hospital, Harvard Medical School, Broad Institute of Massachusetts Institute of Technology and Harvard
Primary contact	Email: saronson at partners dot org
Editors	Liggett, Stephen B.
Year published	2016
Volume and issue	6 (1)
Page(s)	4
DOI	10.3390/jpm6010004
ISSN	2075-4426
Distribution license	Creative Commons Attribution 4.0 International
Website	http://www.mdpi.com/2075-4426/6/1/4
Download	http://www.mdpi.com/2075-4426/6/1/4/pdf (PDF)

Abstract

Academic medical centers require many interconnected systems to fully support genetic testing processes. We provide an overview of the end-to-end support that has been established surrounding a genetic testing laboratory within our environment, including both laboratory and clinician-facing infrastructure. We explain key functions that we have found useful in the supporting systems. We also consider ways that this infrastructure could be enhanced to enable deeper assessment of genetic test results in both the laboratory and clinic.

Keywords: genetic testing process, information technology support, LIMS, LIS, GeneInsight, GIGPAD

Introduction

The clinical genetic testing process within an academic medical center involves multiple different groups. Clinicians identify the need for tests and order them. Then, laboratory technicians receive these orders with associated samples and perform the requested assays. The results of these assays are sent to laboratory personnel responsible for interpreting the results and ultimately producing a report that is signed out by a board certified professional. This report is then returned to the clinician who is responsible for assessing how the results should affect the patient’s care. The clinician shares the assessment with the patient and also stores and manages the results over time.

Each of the groups involved in this process requires information technology (IT) support to perform its function in a high quality, efficient manner. This often involves establishing deep support for specific processes. Multiple systems may be needed to meet a group’s needs. In this context, it is important to determine how systems should be integrated across the workflow. The quality of the overall clinical process depends on data transferring in a robust, consistent manner. Figure 1 shows the infrastructure that we have found necessary to support these process flows in the germline genetic testing environment. There are multiple ways this functionality can be implemented. While a complete review of different methods is beyond the scope of this article, we will describe the infrastructure that we have established to support the clinical germline genetic testing processes implemented by our Laboratory for Molecular Medicine (LMM).

Fig. 1 System functionality required to support the clinical genetic testing process flow

Clinician-facing infrastructure

The electronic health record (EHR) is the basis for most clinical IT support. However, the EHR often has to be extended to provide in-depth support for a particular area or function. As a result, it is useful to think in terms of an EHR ecosystem that includes other systems linked to the EHR. We have found that the clinical genetic IT support needed most by clinicians includes helping them receive and manage genetic test results as well as enabling them to stay up to date on changing genetic knowledge.

Our institution is in the process of transitioning from a custom built EHR to Epic (Epic Systems, Verona, WI, USA). We have integrated an external application we created, GeneInsight Clinic, with both of these EHRs to provide genetics support for our clinicians (Figure 2). GeneInsight Clinic provides clinicians access to easily view genetic test results that have been executed on a patient by our LMM and the potentially meaningful variants that were identified by these tests by incorporating structured data delivered by the molecular genetics laboratory. Users can then drill down into the interpretation of those variants that were assessed relative to the indication for testing. It also provides clinicians with alerts when one of these interpretations is updated by the reporting lab in a potentially clinically significant way. We also recognize the need for additional forms of clinical decision support (CDS) including rules being developed by the National Academy of Medicine’s Display and Integrating Genetic Information Through the EHR Action Collaborative (DIGITizE AC) organized under the genomics roundtable. We have not yet leveraged Substitutable Medical Applications and Reusable Technology (SMART) apps to extend our clinical genetic displays, but we believe this platform has great potential and are investigating doing so.

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In several cases the PubMed ID was missing and was added to make the reference more useful.