College of American Pathologists
Printable Version

  For molecular labs, a sleek new LIS


cap today

February 2006
Feature Story

Ed Finkel

Until recently, molecular diagnostics laboratories that wanted to create a lab information system customized to molecular work, one that addresses day-to-day clinical needs and longer-term research aims, had two choices: build a homegrown system or do their best with pen and pad. Neither handled research efficiently.

But Cerner Corp. and the BloodCenter of Wisconsin say the Millennium Helix system, which Cerner developed in collaboration with the blood center, provides a customized platform that addresses the operational needs of a molecular diagnostics lab and the desire to record data for further analysis. It was unveiled at the blood center in Milwaukee in late 2004.

Cerner now has "three or four active implementations" at sites that include Virginia Commonwealth University in Richmond and ARUP Laboratories in Salt Lake City, says Mark Hoffman, PhD, Cerner’s director of strategy for genomics.

"We’re rapidly gaining traction," he says. "We’ve developed an understanding of which clients are interested in adopting a molecular diagnostics capability. Throughout our development process, we validated our design with them as well" to make sure the solution would be useful in a range of settings.

Helix provides research support by recording pertinent data automatically so users don’t have to do so, Dr. Hoffman says. "It’s associated behind the scenes to a clinical vocabulary," he says. "The day-to-day user isn’t concerned about that. That’s happening without their active involvement."

Embedded within Helix is reference content called the Clinical Bioinformatics Ontology ( that provides a variety of useful capabilities, Dr. Hoffman says.

"It offers, for example, mapping between mutations, gene structures, [and] chromosomes," he says. "For example, if a user wanted to query their data for all results related to chromosome 7, the reference content would support that determination without the users at the bench ever having to specifically document that this mutation is related to chromosome 7."

By associating results to standardized values, Dr. Hoffman adds, it’s easier to compare results between patients, to retrieve specific patient histories, and to exchange data between sites.

Helix is also designed to "move upstream" by documenting protocol and integrating "results generated while you’re, for example, isolating DNA within your sample and specimen management architecture," he says. "The goal of that is to replace the wall of three-ring binders that every lab has with an online documentation tool that can be queried."

In designing the system, Cerner worked most closely with the Blood Center of Wisconsin but also with other laboratories, Dr. Hoffman says. "They are our first development partner," he says of the blood center. "We wanted to make sure it was responsive to their needs and their goals."

"We would walk through their lab, talk about workflow, talk about their current state, and then, based on those meetings, we generated our initial requirements for the functionality," he says. "Then, as we moved forward with our development, we scheduled periodic online demonstrations for them to provide their feedback on our progress."

A 59-year-old organization created to merge science and transfusion medicine and provide blood products, the BloodCenter of Wisconsin had been using a homegrown system before switching to Cerner, says Debra Endean, PhD, vice president of the blood center’s diagnostic laboratories. No system easily met the center’s needs because transplantation tests, which make up 40 percent of its business, require information from multiple donors, family members, and patients to be integrated, something the typical one-patient-one-result system does not support.

Daniel Bellissimo, PhD, director of the center’s molecular diagnostics lab, says the blood center, which performed 69,000 tests and distributed 237,000 units of blood and blood products on an $85 million budget in 2004, has been using Cerner’s Millennium PathNet laboratory system since 2002. That represented an improvement over the previous method of writing reports in Microsoft Word but still required too much manual entry of information. Helix fills in negative mutations automatically, a significant time-saver, he says.

Millennium also did not provide as much flexibility to construct reports, especially on the genetics side, Dr. Bellissimo says. "Our laboratories went through a big search initially because we have so many different laboratories here with so many different needs," he says, referring to the original Millennium purchase. "At the end of 2004, we converted one of our tests to Helix, and we’re building all new tests there. We started off with some simpler tests to get familiar with the platform, and now we’re working on some of our more complicated tests."

Among the most useful features thus far has been Helix’s built-in linkage between genetic results and genetic concepts, Dr. Bellissimo says. "It’s linking everything back to the genome. It makes it easier to build a test in the system because the genes and their mutations are already there," he says. "Linking the results to a common genetic concept is important because you share information more easily with other Helix users." Even if a data element is called by a different name, the data are all linked to something in common.

The system’s Unified Case Manager, or UCM, enables users to view simultaneously all the tests ordered on a single patient and see where they are in process, which the blood center also has found valuable, Dr. Bellissimo says. UCM is also a common launch point for most of the system’s applications.

"The Helix system has ways of having multiple workups on a patient," he says. "If patients had multiple test orders placed on their samples, you would be able to see all the orders.... We’ve defined different workups based on different sample types. We can actually build a test in the system such that there’s a workup for each of the possible sample types, such as blood, tissue, or amniotic fluid." When staff in the client services department receive the sample, "they don’t have to worry about whether I have ordered up the correct procedure."

The blood center also has been able to build into each workup "hidden" orders that can be activated as needed, Dr. Bellissimo adds, which had required toggling to a separate application in the previous Cerner system. "This way it’s pre-built and hidden, easy to activate—a big improvement."

Another new application the BloodCenter of Wisconsin has found helpful is the case integration function that enables users to construct a report, built out in sections, with separate comment screens related to specific genetic test results, Dr. Bellissimo says.

"You could have a button for a certain test result, and behind it are all the comments," he says. The application makes it "easy to construct a report based on test results. ... They’re working on a lot more formatting in those text areas."

Virginia Commonwealth University, which developed a homegrown system 15 years ago, expects to upload Helix in late summer, says Andrea Ferreira-Gonzalez, PhD, professor of pathology and director of the molecular diagnostics laboratory.

While the homegrown system has made it possible to automate testing and information management, she says, it has been limited in terms of both flexibility, because it’s constructed within Microsoft Access, and stability, because of the need to update it internally as new technologies and tests require.

Gregory Miller, PhD, professor and director of pathology information systems at VCU, says the design of the Helix architecture will give them greater flexibility to adapt to the rapid change in technology in molecular diagnostics testing. "It will be more sustainable in the long term over a custom database," he says.

A software package from a major vendor ensures long-term sustainability and portability of the solution, he notes. "You get the benefit of a large engineering group, and you get the benefit of integrated solutions." That obviously costs money, he adds, but with the custom Access solution, "we would carry the burden of rewriting it as new functionality was required." Helix will create "a more seamless process" for VCU, says Dr. Ferreira-Gonzalez, by providing a single solution where all data that are required and generated as part of the testing process are kept electronically—everything from the tests that have been ordered, the protocols performed, and QC data, to the generation of final reports.

"It will allow us to have electronic management of the data," she says. "It will allow us to decrease the number of steps we have to manipulate the data to create a report. It will allow us to be able to work with a variety of platforms and operating systems and converge all the data in a single place."

Dr. Miller says Helix will be integrated with the rest of the LIS as well as the hospital’s Cerner Millennium clinical system, and it will place individual test results within the database as discrete elements recognizable as data. Results in the electronic medical record that originate from the homegrown Access system are text strings that "can’t be searched, can’t be aggregated for purposes of trend evaluation," he says. "Those will be significant improvements."

Another benefit for VCU: the ability to run expert rules to aid physician ordering and results interpretation. "We can give them heads-up information that a genetic test has already been done, [so] you don’t have to do it again," Dr. Miller says. In time, Helix will also make it possible to provide pharmacogenetic advice for ordering of drugs. "It will enable the whole expert rules guidance-pathways to be created for physician education and information," he says.

VCU plans to train all its technicians and technologists on the new system but does not expect the training to be any more complicated than that of a typical LIS conversion, Dr. Ferreira-Gonzalez says. "Our medical technologists are used to working with different laboratory information systems. For others who don’t use an LIS, [the initial conversion] might be more of a problem."

She estimates that 95 percent of the laboratories performing molecular diagnostics now have little input into their information system. "The majority of the work and documentation is done on paper, and you can start imagining the burden of this process and some of the problems" it can create. For these labs, Helix represents "a huge improvement," Dr. Ferreira-Gonzalez adds. "It will help improve efficiencies and reduce the possibility of errors."

Even those molecular diagnostics laboratories that now use general laboratory information systems will see gains with Helix, Dr. Miller predicts. "If you don’t have anything, and you’re trying to shoehorn molecular results into a general laboratory framework, there are a lot of difficulties in the way results are reported," he says. "There wouldn’t be a whole lot of support for workflow and virtually no support for automation of results, which is one of the features that Helix is going to provide."

In the future, the BloodCenter of Wisconsin hopes to work with Cerner to build in additional functions, such as the ability to integrate protocols, Dr. Bellissimo says. "We’re working to connect the laboratory data to the test result in the system, such as a gel image," he says. "They’re looking at ways of linking data to get pedigrees."

The blood center also hopes to boost the reporting functionality with regard to red cell antigen testing, which comes up most commonly in the case of maternal-fetal incompatibility. "A lot of times we’re doing multiple tests for multiple antigen systems," Dr. Bellissimo says. "Now, we use built-in comments, but we have to report each test individually." Once they build those tests in Helix, it will be possible to integrate those test results, so they will be able to generate a much clearer report for physicians, he says.

As these functions unfold, Dr. Bellissimo hopes other laboratories within the blood center will be able to take advantage of such applications as being able to take multiple test results and create a report with a final interpretation. "They’re just waiting for the molecular lab to lay the groundwork for this," he says. "Our LIS staff will apply what we learned to our other labs."

Cerner markets a separate histocompatibility module with which the Helix is designed to be compatible and complementary, Cerner’s Dr. Hoffman says. "The HLA solution has been marketed for more than five years and is used widely within that niche," he says, noting that the blood center has it. "That’s part of why they were a very appealing development site—they had a mature Cerner footprint, including HLA.

Cerner has incorporated a lot of new knowledge into Helix, Dr. Hoffman says. "HLA meets the needs of the histocompatibility labs very well, but it doesn’t have some of the bioinformatics capabilities that Helix does." By designing Helix so that it’s compatible with the HLA solution, Cerner is chipping away at the research concerns that have cropped up along the way.

Ed Finkel is a writer in Evanston, Ill.