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April 2008

Molecular, Genetic Data and the LIS By Dennis Winsten As Dr. Alexis Carter noted in her ADVANCE article, "The demand for laboratory tests performed by molecular methods is increasing at a rapid rate; several hospitals have reported increases from 6 percent to 25 percent per year. The unique nature and newness of molecular techniques have resulted in a relative lack of adequate information management tools. However, the expectation that this rise in test numbers will continue for the foreseeable future is putting pressure on vendors to supply laboratories with information systems that can meet their specific needs. Several molecular information systems are commercially available, each with varying capability to meet these needs." 1 In keeping with that prediction, 2007 saw continued evolution of LIS applications for molecular diagnostics (MDx) and genomic applications. Cerner and SCC Soft Computer were initial developers;2 additional firms have followed suit. Some have developed unique software especially for MDx/genomic applications; others are using enhanced

features of their clinical and anatomic pathology applications to serve the information processing needs of MDx/genomics. The emphasis of the union of radiological and imaging techniques to complement the processing and reporting of results is also emerging. An Evolution Cerner Corp., whose Millennium Helix application was the earliest developed, has continued evolution of its product. Millennium Helix was first used for patient testing at the Blood Center of Wisconsin in 2004.2 To date, more than 25 organizations, including large and small reference labs, academic medical centers, pediatric hospitals and large federal organizations use it. The system was designed to support the rapidly evolving areas of molecular testing-- genetic testing, cytogenetics, flow cytometry and molecular detection and classification of pathogens. Modules support discrete result entry, protocol worksheet documentation, flat file import and exports, template-based report generation, rtf pre-defined

layout style reports, karyotype result entry and sample management. While the past year has been dedicated to strengthening the ability to support flow cytometry and cytogenetics labs, the most significant innovation has been a unique karyotype editor that promotes compliance with ISCN and parses karyotypes into easily searchable and coded concepts. In conjunction with Helix, Cerner has developed the Clinical Bioinformatics Ontology (CBO) to standardize molecular findings. The CBO has nearly 12,000 unique concepts. Results are standardized using the CBO, promoting extensive analytical capabilities. Millennium Helix also promotes the comparison of results between patients, for example, to support family member comparisons. Millennium Helix also provides context sensitive links to OMIM (Online Mendelian Inheritance in Man) and the NCBI as appropriate. The OMIM database is a catalog of

textual information and references about human genes and genetic disorders authored and edited at Johns Hopkins and elsewhere, and developed for the Web by the National Center for Biotechnology Information (NCBI). Advancements this year included workflow-related enhancements, such as the ability to automatically reorder sample processing steps when a downstream step fails. Additional planned enhancements include:

SoftFlowCytometry interfaces with flow cytometry instruments for rapid data capture, scatterplot images and customizable sample processing workflows and task lists. The module provides various data management tools, sample processing worklists, analysis, interpretation, management reporting and billing. SoftMolecular provides interfacing with sequencing and fragment analysis instruments, daily manager · worklist queues accessible throughout the research and testing lifecycle and real-time inventory control with user · trackable worksheets. Intuitive workflow tracks cases through DNA/RNA · determination, amplification, detection and interpretation. Graphs, video and audio files depict visible test results and a history of the sample at each stage. Reporting is through the use of online worksheets. Shared Infrastructure NeTLIMS offers AutoGenetics, a merger and shared infrastructure between its general lab and anatomic pathology modules, AutoLIMS and AutoAP. The AutoGenetics application is focused on workflow optimization and "reflexes" next steps based on the process and intermediate outcomes. AutoGenetics is intended to support MDx and cytogenetics. It integrates with the entire AutoLIMS product suite, sharing catalogs

and basic functions (Web access, auto-fax, etc.). XSL is used as the layout language for reports, allowing flexibility for case, result and client-specific report formats. Features include: online storage of accompanying images and external documents and the ability to incorporate into the result report; onscreen case review, editing, electronic signature and double signature support based on case information; multiple result entry modes supported, including template-based word integration; flexible work assignment through user-defined roles and role holders; and extensive security/permission levels, including individual, actions permitted, test access permitted. Clinical Solutions McKesson's Horizon Lab customers use existing functionality within the LIS to report molecular test results to clinicians. McKesson is in the process of developing clinical solutions that incorporate genetic information into the clinical workflow. The intent is to enable providers to use that information in a structured format for pharmacogenomics, disease stratification, risk interpretation, order appropriateness and recommendations and disease prevention. The genetic information will be


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the ability to integrate images into workflow and reports, generation of advanced statistical reports and continued developments to promote automated workflow. Modality-specific Modules SCC Soft Computer, another early entry into the MDx/genomics LIS arena, offers a set of modalityspecific modules for cytogenetics, flow cytometry and molecular testing. SoftCytogenetics, for example, provides Web-based access to managers' dashboards for tasks and workload tracking and flexible templates for reporting by sample type. The cytogenetics module allows processing of cases using workflow scenarios as determined by the laboratory (SOPs), including culture setup through harvesting, slide processing, analysis and reporting.

maintained alongside other relevant patient information and linked where appropriate to standardized vocabularies to be maintained over the course of a patient's lifetime. Rules-based Technology Molecular testing generates several types of results in various modalities-- quantitative, cytology, pathology or microbiology interpretive text and, increasingly, related images. One common molecular report is the combination of cytology and molecular tests that have been routinely performed and reported separately. An example of this is the liquid-based Pap test combined with an HPV result. Most pathologists agree that these tests should be reported together on a single report. To produce a hybrid report that can easily consolidate any combination of these result types, Orchard Software Pathology AP system uses its rules-based decision-support technology, employing formulas to trigger specific interpretative text that streamlines the process of formatting a report to a specified design. Images representing the interpretation are linked to the AP worksheet and added to the report. Multiple images can be added to the report, displayed in either a vertical or horizontal format. More Informative Reports

Sunquest Information Systems is extending the integration of its clinical laboratory system with Sunquest CoPathPlus and is working on new reporting capabilities that will enable customers to combine clinical, pathology and molecular-based results into a single, more informative report to support more knowledgeable clinicaldecision making (e.g., a report with HPV molecular-based test results and Pap smear along with the pathologist's interpretation). Sunquest Information System's customers utilize CoPathPlus for cytogenetic analysis and in conjunction with Sunquest's partner, Apollo, image storage. In addition, Sunquest provides interfaces to more than a dozen instrument systems that are molecular-based. This list is continuing to expand in response to increasing requests for connectivity to systems for molecular testing. A Union With Imaging Vendors and other experts predict an integration of imaging and classical laboratory reporting. Bruce A. Friedman, MD, active emeritus professor, Department of Pathology, University of Michigan Medical School, has begun to use the term in vitro/in vivo diagnostics (IV2D) to refer to the blending or even merger of the clinical labs, pathology and radiology. "The ultimate

goal of such an organizational change would be to facilitate the emergence of a new breed of specialist, the diagnostic hybridist, to diagnose disease, assess the prognosis of disease and assist clinicians in their choice of therapy."3 Dr. Carter agrees. "Image storage is becoming an increasingly important component of all information systems, and an LIS for molecular laboratories is no exception. Many molecular laboratories still take photographs of gels for documentation and store those photos either on paper or in an imaging system that does not communicate with the general LIS. The ability to incorporate images into reports is starting to take off; molecular laboratories will benefit from this capability by incorporating gel photographs as well as images of sequencing or real-time PCR data into reports."1 Clearly, the rapid advancement and growth of molecular testing has stimulated considerable interest by LIS vendors. Still, for most, it is early in the software development cycle and decisions are being made regarding the best approaches to enhanced/extended clinical applications and new, unique molecular testing methodologies. Likewise, the linkage to databases of relevant genetic and/or pharmacogenetic databases continues to be a work in progress.



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