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Cerner Readies Upgrade for Helix Clinical Genomics Software as NCI Adds its Ontology to Metathesaurus


Healthcare IT firm Cerner isn't known for its bioinformatics activities, but a year after the launch of its first clinical genomics software, the company appears to have secured a solid foothold in the sector.

The Kansas City, Mo.-based company, which generated more than $1.3 billion in revenues last year on the strength of its Cerner Millennium medical records management system, has recently entered into a partnership with Virginia Commonwealth University to develop new capabilities for its clinical genomics software. The software was launched under the name of PathNet Helix last March [BioInform 03-07-05], and is now known as Cerner Millennium Helix for Laboratory.

In addition, the company's Clinical Bioinformatics Ontology, or CBO — a controlled vocabulary that serves as the foundation of the Helix product — will soon be included as part of the National Cancer Institute's Metathesaurus, according to Mark Hoffman, genomics solution manager at Cerner.

Cerner developed CBO in order to bridge biological concepts from medical vocabularies and bioinformatics resources like RefSeq. The ontology currently includes around 7,000 concepts and more than 16,000 relationships between those concepts. It has grown since it was launched last year to include more concepts related to cytogenetics, disease, and major alleles and mutations for genes of interest to pharmacogenetics, such as the P450 family.

"Helix is promising to let us run our molecular lab a little bit more like we need to, and still do the clinical reporting function."

The NCI Metathesaurus, developed and maintained by the NCI Center for Bioinformatics Enterprise Vocabulary Service, currently contains 850,000 concepts mapped to 1.5 million terms by more than 4.5 million relationships.

Sherri de Coronado, EVS project manager at the NCICB, confirmed by e-mail that Cerner's ontology is included in the NCI2005_10E version of the Metathesaurus, which is scheduled to go into production on March 3.

CBO "complements" the biomedical vocabularies that are already in the resource, she said. "It shares some concepts with other vocabularies, and is mapped to those concepts where appropriate, but contains much more precise terminology related to gene and protein sequences, focusing on clinically useful sequence variations in a systematic way … and providing semantic linkages between concepts that are not provided by other vocabularies."

The CBO is also freely available at a dedicated website (, where registered users can download the ontology in several formats.

"We're still doing the curation work, but [NCI will] take periodic updates of the CBO and load it into their resource, so we see that as major validation that what we're doing is indeed novel and useful," Hoffman told BioInform.

Hoffman said that around nine organizations have agreed to add Helix to their current Millennium system during the last year, and "at least half of those are in active implementations right now."

In addition to VCU, the Blood Center of Southeastern Wisconsin and ARUP Laboratories, a large reference lab based in Salt Lake City, have implemented the Helix system, he said.

Cerner is not the only organization developing informatics tools for clinical genomics. IBM launched its own data-integration platform targeting this market, dubbed the Clinical Genomics Solution, in 2004, and so far counts the Mayo Clinic, the University of Utah Health Sciences Center, and the University of Montreal's Mother and Child University Hospital Center among its customers for the system.

In addition, the NIH tapped a clinical genomics project led by Isaac Kohane at Brigham and Women's Hospital for its first round of National Center for Biomedical Computing Roadmap grants in 2004. The so-called i2b2 (Informatics for Integrating Biology and the Bedside) center is developing "a scalable informatics framework that will bridge clinical research data and the vast data banks arising from basic science research in order to better understand the genetic bases of complex diseases," according to its website.

The field has also attracted the interest of smaller firms like Ardais and PointOne Systems, which specialize in informatics systems at the interface of clinical medicine and genomics.

But none of these companies has what Cerner has — an installed base of approximately 4,800 Cerner Millennium systems at more than 900 medical centers, clinical labs, and hospitals that are looking for ways to incorporate information from a growing number of molecular diagnostic tests into their traditional clinical IT systems.

Millennium Helix for Laboratory promises to offer this capability. It is a module that plugs into the Millennium framework that enables clinical labs to integrate molecular diagnostic data — including hybridization results, DNA sequence data, and gene expression analysis — with electronic medical records.

Brian Jackson, medical director of informatics at ARUP, described the facility as a "straight clinical lab" that was looking for software to address some of the unique challenges of its molecular diagnostics group. "The workflow is more complicated" in the molecular lab, he said, "and we're hoping that Helix will help manage that better. The reporting is more complicated for molecular testing, and we're hoping that in the long run we'll have more flexible reporting."

In particular, Jackson said that ARUP expects Helix to help manage its sequence data, which is currently held in a homemade database that is separate from the rest of the laboratory's clinical information management system.

Jackson stressed that ARUP is still in the middle of implementing Helix, and doesn't anticipate the system to go live until the fall. He said that the lab considered other options, primarily LIMS, for handling its molecular diagnostic data, but opted for Helix because "we weren't looking to go for a research-type of laboratory information management system — we really wanted to stick with the clinical lab products, and Helix is promising to let us run our molecular lab a little bit more like we need to, and still do the clinical reporting function."

While the initial uptake for Helix isn't skyrocketing, Cerner's Hoffman said that he's "pleased with the adoption" so far.

"One nice thing about the stage we're at right now is that we have representation from the different types of adopters," he said, noting that the company has so far implemented the system at mid-sized reference labs, academic centers, and larger labs like ARUP. "We really are reaching the point where we have the experience of implementing in a variety of settings."

Hoffman said that new features that Cerner is adding to the system in collaboration with VCU include enhanced capabilities for cytogenetics, and a flat file import/export feature that is expected to improve interoperability with diagnostic instruments.

"Most of the diagnostic devices in the molecular lab are not able to interface with clinical information systems, so this flat file import and export is a way of providing a near-term measure to still offer some automation," he said. "It's not a formal interface, but it's a capability that will certainly save a lot of time for people in the labs."

In addition, Cerner is improving the "protocols functionality" of Helix in order to "replace the wall of three-ring binders that every lab has with an online capability." This feature is envisioned as a template for designing experiments such as PCR runs in order to automate many manual tasks. "By doing that online, that puts it in an environment where you can run queries," Hoffman said, "so if you structure your worksheet to include the lot number of an enzyme, and you get a recall notice, you can rapidly identify cases that may have been affected by that defective enzyme."

While Hoffman hesitated to describe the system as a LIMS, he said it "certainly takes us closer to that arena within the context of the diagnostic setting."

Hoffman said that the first release of Helix with these new features should be available by the spring.

— Bernadette Toner ([email protected])

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