A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record

Abstract

Purpose: Genome-scale clinical sequencing is being adopted more broadly in medical practice. The National Institutes of Health developed the Clinical Sequencing Exploratory Research (CSER) program to guide implementation and dissemination of best practices for the integration of sequencing into clinical care. This study describes and compares the state of the art of incorporating whole-exome and whole-genome sequencing results into the electronic health record, including approaches to decision support across the six current CSER sites.

Methods: The CSER Medical Record Working Group collaboratively developed and completed an in-depth survey to assess the communication of genome-scale data into the electronic health record. We summarized commonalities and divergent approaches.

Results: Despite common sequencing platform (Illumina) adoptions, there is a great diversity of approaches to annotation tools and workflow, as well as to report generation. At all sites, reports are human-readable structured documents available as passive decision support in the electronic health record. Active decision support is in early implementation at two sites.

Conclusion: The parallel efforts across CSER sites in the creation of systems for report generation and integration of reports into the electronic health record, as well as the lack of standardized approaches to interfacing with variant databases to create active clinical decision support, create opportunities for cross-site and vendor collaborations.

Figure 1. This figure created by the National Institutes of Health Clinical sequencing exploratory Research (CSER) electronic Medical Records Working Group (EMR WG) shows the typical CSER site workflow from specimen acquisition through the reporting of whole-exome or whole-genome results into the EMR

As described in the text, each of the six CSER sites has its own site-specific workflow and its own variant database/knowledge base. The focus of the CSER EMR WG (and the survey presented in this article) is indicated by the shaded areas of the figure.