CAP TODAY Pathology/Laboratory Medicine/Laboratory Management
Why LIS limitations shouldn’t inhibit genomic testing
Many community-based hospitals don’t have the resources to perform complex genomic testing, but they shouldn’t let that deter them. By being creative in overcoming the limitations of their lab information systems, pathology departments can ensure that clinicians and their patients benefit from the latest advances in next-generation sequencing, says Lynn Bry, MD, PhD.
“When you’re looking at complex molecular testing, none of the clinical LISs are particularly well designed to handle it,” says the associate professor of pathology at Harvard Medical School and director of the Center for Clinical and Translational Metagenomics at Brigham & Women’s Hospital. For a pathology department seeking to bring genomic testing in-house, “in addition to the investment in sequencers, technical personnel, and your bioinformatics team, you also need to make investments in how you integrate those pieces with the LIS, because outside of the upfront sample handling and getting results out the door and billing for it, you probably aren’t going to be able to handle the intermediate steps with current lab information systems.”
The simplest way for a pathology department at a smaller institution to offer genomic testing is to contract with a reference lab that will do the testing and interpret the results, says Dr. Bry, who gave a presentation on pathology systems to support genomic medicine at the Pathology Informatics 2014 conference, in May. “The pathology department should educate the clinicians as to what the tests do, their strengths and weaknesses, and make certain they understand how they’re going to use the data,” she adds. “They shouldn’t just make the tests available.”
In this scenario, says Dr. Bry, the LIS receives the test results and interpretation that will be reported to the clinician. “The simplest method is sort of a pass-through, which they could potentially use for germline genomics: the LIS receives a glob of data as an unstructured report, which is not particularly elegant but at least gets the data back to the clinician.” A better approach, she maintains, is to “put some thought into it and structure the variants in some way so you can at least say, ‘The patient had these variants; these were graded as normal, or not normal,’ etc.” Unfortunately, however, very few commercial LISs are set up to receive structured information, she notes. To get around this problem, pathology departments with the right IT expertise can build their own tools to structure the information. For others, “kind of an in-between is to receive the information as a PDF file within which the information is structured. That way, you can at least load it into the LIS, and if, at a later date, you need to go in and extract structured information, you can do it. You don’t have to build de novo tools.”
“A lab could use HL7 to send to and receive data associated with complex genomic tests from the reference lab conducting the testing,” Dr. Bry adds. “Decisions to go this route would depend upon the degree of integration desired, which is often driven by the volume of testing, cost to do the integration, and if the HL7 stream could piggyback on something already in place with the reference lab or would require a new interface.”
Another option is to invest in a platform that allows for a high-demand test to be performed in-house. In cancer testing, for example, vendors such as Ion Torrent and Illumina are developing platforms similar to black box systems, Dr. Bry says. “They’re not a true black box like a chemistry analyzer, but they have more automation with the data interpretation than other types of assays.” An institution focused on lung cancer, for example, “can or may soon be able to invest in panels you could run locally in your lab, to look at select variants that could help with diagnosing the tumor as well as selecting particular therapies. That would be the initial first step, rather than doing a large, complex panel or exome, or even a genome.”
But again, integrating the data from the test into the existing IT structure poses a challenge. A lab might well be able to handle the technical preparation and conduct the testing but lack the bioinformatics expertise to interpret the test results. “So all the bioinformatics would be tracked on the vendor platform, but you yourself, in the lab, would have to figure out a way to get that information into a report that you’re sending out through your LIS,” says Dr. Bry. Some labs might have the internal expertise to make that connection, “or you would have to contract with the vendor giving you the box, or the LIS vendor, or another vendor, to get it set up for your lab.”
While LIS vendors may be considering how to update their systems to support genomic testing, Dr. Bry says, “I haven’t seen any of the vendors coming forward to say, ‘Here’s a solution that’s going to help you with your complex genomic testing.’” Some companies have developed laboratory information management systems to support complex sequencing in a research setting, “but what they often lack is the capacity to operate effectively in a CLIA laboratory,” she explains. “They’re not used to tracking the necessary quality control or other metrics you’d want in a clinical LIS.”
Contracting with a reference lab may be the best solution for now, Dr. Bry says. It allows a pathology department to gain experience with the data that’s returned, and then, “as [testing] volumes grow and dynamics change, you can evaluate if platforms have matured enough for you to do testing locally, or maybe you outsource the technical piece and then decide if you want to evaluate the variants that come back.” —Jan Bowers
Cerner to purchase Siemens’ health IT business unit
Cerner has signed a definitive agreement with Siemens to acquire the assets of Siemens’ health information technology business unit, Siemens Health Services, for $1.3 billion in cash. As part of the agreement, Cerner and Siemens will form a $100 million strategic alliance to bring to market solutions that combine Cerner’s health IT leadership and Siemens’ strengths in medical devices and imaging.
“Siemens’ health care IT assets provide additional scale, R&D, an impressive client base, and knowledgeable and experienced associates who will help Cerner achieve our plans for the next decade,” Cerner CEO Neal Patterson said in a statement. “In addition, the alliance we’re creating will drive the next generation of innovations that embed information from the EMR inside advanced diagnostic and therapeutic technologies, benefiting our shared clients.”
According to 2014 estimates, Cerner and Siemens Health Services combined have over 20,000 employees in more than 30 countries, 18,000 client facilities, and generate $4.5 billion in annual revenue. Following the acquisition, support for Siemens Health Services’ core platforms will remain in place and current implementations will continue. Cerner plans to support and advance the Soarian platform, including the Soarian Clinicals EHR, for at least the next decade.
Meanwhile, Cerner and Siemens reported that they will jointly invest in projects that integrate health IT with medical technologies. Each company will initially contribute up to $50 million to fund the projects over a three-year period. The inceptive focus will be on advanced workflows and medical imaging.
The acquisition is expected to be finalized early next year.
Cerner, 816-221-1024
Siemens, 800-743-6367
Brunston system provides patient access to test results
Brunston Corp. offers a patient laboratory report access system that gives patients direct access to their lab test results as printable reports and voice summaries.
Patients can access PDF report files of their test results on the system’s website or receive the reports as encrypted email. The system generates security tokens and S/MIME certificates as needed.
Brunston’s report-generation process creates lab reports from HL7 files transferred from client EMRs via secure data interfaces. It merges partial reports and corrections as they arrive.
“Patients are provided Web accounts and individual secure email addresses at no cost to them,” says Donald Butler, PhD, president of Brunston. “Patients less comfortable with computers can be mailed or handed printouts of the reports.” Patients are also provided several U.S. or Canadian telephone numbers that they can call to access summaries of their test results and related information.
Physicians have the option of offering multilingual reporting, which lets their patients choose from select languages when calling to obtain test results and other information. Patients too can receive appointment reminder notifications by telephone in one of several languages.
Brunston Corp., 208-968-7770
Private equity firm buys Xifin
The private equity firm GTCR has acquired Xifin, a provider of cloud-based health care software and services.
“Our history of successful investments in diagnostic laboratories and SaaS-based software providers will enable us to help fuel the next phase of Xifin’s growth,” says Ben Daverman, vice president of GTCR.
Xifin’s core product is a cloud-based application for billing and collections that automates billing workflow. Xifin also markets a cloud-based laboratory information system, physician and patient portals, enterprise class business intelligence solutions, and a physician collaboration network.
“Xifin remains deeply committed to the markets we serve and to expanding our investment in our customers, technology platform solutions, and employees,” says CEO Lale White.
Xifin, 858-436-2995
Orchard releases new version of Copia integration engine
Orchard Software has introduced Orchard Copia version 6.0, the latest release of its SQL-based, lab/EHR integration engine designed for complex outreach business scenarios.
Among the enhancements in Copia version 6.0 are:
- Microsoft’s SQL Server Reporting Services server-based report-generation software. SSRS works with an interface to Microsoft Visual Studio in conjunction with Copia, allowing users to create content-rich reports, with graphics, from the data contained in a lab’s Copia application.
- An option that allows users to create and edit custom patient and order menus.
- An application called Labeler, which provides advanced support for remote label printing. Labeler generates its own labels and sends them, as images, to the label printer, allowing the latter to print bar codes.
- Improved search functionality that allows pop-up and predictive searching. When a user begins typing search criteria, the application suggests topics based on what is being entered.
- Upgrades to the Copia Mobile module that enable it to generate collection lists.
- Support for Gmail email communications.
Orchard Software, 800-856-1948
GenoLogics introduces updated Clarity LIMS offering
GenoLogics Life Sciences Software has announced the availability of Clarity LIMS 3.1, the latest version of the company’s lab information management system for omics labs.
Version 3.1 adds features that support safety and security, including electronic signature capability, configurable permissions, and detailed audit trail reporting.
“We are proud to release version 3.1 of Clarity LIMS and further support compliance requirements,” says GenoLogics CEO Michael Ball. “These features reiterate our dedication to make next-generation sequencing a mainstay in clinical environments.”
GenoLogics Life Sciences Software, 866-457-5467
NovoPath announces support for Primera medical printers
NovoPath has added Primera Technology’s Primera Signature printers to the roster of specialty laboratory label printers it supports for its NovoPath anatomic pathology system.
The Primera printers automatically print labels directly onto laboratory slides and cassettes. The labels may include high-resolution color, text, graphics, and bar codes suitable for automation.
NovoPath, 877-668-6123
Primera Technology, 800-797-2772
[hr]Dr. Aller is director of informatics and clinical professor in the Department of Pathology, University of Southern California, Los Angeles. He can be reached at raller@usc.edu. Hal Weiner is president of Weiner Consulting Services, LLC, Florence, Ore. He can be reached at hal@weinerconsulting.com.