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Hospitals Lagging in Using Discrete Genomics Data for Clinical Decision Support


CHICAGO (GenomeWeb) – As US healthcare organizations move into clinical genomics and build bioinformatics pipelines, many are lagging when it comes to integrating structured data into their electronic health records.

This shortfall means that few institutions are able to incorporate genomics into clinical decision support, according to a preliminary survey of participants in the National Human Genome Research Institute's Implementing Genomics in Practice (IGNITE) program.

Researchers representing four prominent provider organizations presented their findings in a poster at the American Medical Informatics Association annual conference in San Francisco last week.

In a survey of the 13 IGNITE sites, the researchers found that while all performed internal clinical germline genetic testing and all but one used outside labs for some genetic tests, only seven had developed their own bioinformatics pipelines with structured data to inform clinical decision support — chiefly from internal reports. Just a third of those queried had external structured results in their EHRs even though all were able to receive outside reports electronically.

Of the 13 IGNITE sites, 92 percent were performing local genetic testing for pharmacogenomics, 69 percent for infectious agents, 62 percent for rare pediatric conditions, and 54 percent for rare adult diseases. Some 46 percent ran in-house prenatal genetic tests, the poster showed.

"This is in-progress research to get a cross-sectional look at US-based institutions to look at how sophisticated and how comprehensive their pipeline is to bring genetic data from the instrument to the point of care," explained lead author Josh Peterson, an associate professor of biomedical informatics at Vanderbilt University Medical Center.

In addition to Vanderbilt, survey partners represented the Veterans Affairs Salt Lake City Health Care System, Indiana University, and the H. Lee Moffitt Cancer Center in Tampa, Florida. The current IGNITE pool, officially known as IGNITE II: Pragmatic Clinical Trials Network, consists of 10 academic medical centers, one community-based health system, one pediatric hospital, and one independent clinical laboratory.

"All of these [centers] have some element of implementation done there. Most of them are trying to do it the right way, which is with structured data," Peterson said.

"But some of them take what's off the machine, do a written interpretation, and they put it right into the EHR, and it's not always structured," Peterson said. Others manually add structure to certain variants, which can be labor-intensive, incomplete, and prone to error.

Those two-thirds of IGNITE sites not informing clinical decision support with discrete data from outside labs are receiving external sequencing results as noncomputable PDF files or even faxes. Ideally, they would use Health Level Seven International's FHIR Genomics standard, an offshoot of the Fast Healthcare Interoperability Resources specification for exchange of structured health data.

Peterson said that Vanderbilt uses the HL7 2.5.1 standard for internal communication of genetic test results, but does not yet receive external reports in a computable format, he said. "We'd like to be able to get there, but we simply haven't been able to get to the work," Peterson said.

Vanderbilt switched to a new Epic Systems EHR a year ago and has been busy with all the optimization that entails. Medical informaticians have been swamped with interoperability challenges at all levels, and genomics has not been the top priority. "There's just a huge backlog of projects to do," he said.

For the poster presented at AMIA, researchers conducted their preliminary survey earlier this year with a one-page questionnaire, and only included IGNITE sites because clinical genomics has not fully made it into many community, specialty, and critical-access hospitals. "We've thought about doing a random sample of US hospitals, but we just figured that it's probably going to [have] a lot of null results," Peterson explained.

Peterson and colleagues now are circulating a longer, more detailed survey, to involve participants of the Electronic Medical Records and Genomics Network (eMERGE) and Clinical Sequencing Evidence-Generating Research (CSER2) Consortium in addition to the IGNITE cohort.

"Now, we're trying to get into a lot more details about reinterpretation issues and report generation, and we'll hopefully have a bigger sample of whether people do clinical decision support and what kind ... they do with the genetic data," Peterson said. He expects to have more data within six months.

Peterson said to expect only half to three-quarters of this expanded group to have clinical decision support from discrete genomics data. "There are some institutions that don't have the IT infrastructure or don't have the IT staff to really do it justice," Peterson said. "Particularly with some of these more specialized functions like reinterpretation, that's going to be a very small fraction of the people we survey."

NHGRI established IGNITE in 2013 to develop new methods for implementing genomic medicine in diverse clinical settings outside of specialized care and to disseminate its findings to the genomic medicine community. IGNITE II followed in 2017 to run pragmatic clinical trials of genomic medicine interventions previously demonstrated to be feasible and of potential value in clinical care.