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In molecular testing labs, gaps between actual and desirable LIS capabilities

December 2018—Flashback to 2013: Alexis B. Carter, MD, then director of pathology informatics at Emory University Hospital, was contemplating whether other pathology labs nationwide were facing the same challenges managing molecular testing data as she and her colleagues. So she decided to find out. Dr. Carter conducted a survey, and the responses confirmed her suspicions: Most laboratory information systems fall short in providing the infrastructure for complex molecular and genomic testing.

Five years later, Dr. Carter and Charles Myers, MD, and Matthew Swadley, MD, who, as residents in the Department of Pathology and Laboratory Medicine at Emory, had collaborated with Dr. Carter on the survey, shared their findings in the Journal of Molecular Diagnostics (2018;20:591–599).

Priorities at work and other commitments delayed publication of the findings, says Dr. Carter, now pathology informaticist at Children’s Healthcare of Atlanta. However, informal conversations she and her coauthors have had with molecular pathologists indicate that the results are still as relevant today as they were nearly six years ago.

So how did Dr. Carter go from pondering to publishing? She designed a 34-question online survey and sent it to members of the listservs of the Association for Molecular Pathology, American Society for Histocompatibility and Immunogenetics, American Medical Informatics Association, and Association of Pathology Informatics.

To encourage open, honest responses, the survey was constructed to protect the identity of the participants and the brand names of the LISs that were being evaluated. The questions focused on the size of the organizations, number of LISs the respondents used, and system capabilities.

“We also asked about the type of information system they were using,” Dr. Carter says. “Was it something they developed at their institution, a custom-built LIS, was it an information system that was specifically designed for molecular and next-generation sequencing laboratories, or was it a clinical laboratory system they were using as best as they could, or some other system?”
The authors targeted professionals involved in molecular testing, including those who perform transplant molecular diagnostics. The majority of survey respondents were laboratory staff supervisors and medical directors.

“The fact that we had 80 people fully complete the survey [out of 142 who started it] shows there was a high degree of interest in this topic,” says Dr. Carter. The length of the survey may have discouraged some of the initial 142 respondents from completing it, she adds.

The responses of the 80 participants revealed significant gaps between actual and desirable LIS capabilities. “To me, the biggest concern is the fact that a large percentage of laboratories reported having instruments and software in the laboratory that [are] not compliant with the HIPAA final security rule,” Dr. Carter says. “The challenge is that laboratories don’t always know to ask some of those questions because they assume that if a vendor is selling an instrument for this medical purpose, the instrument is going to be compliant by default.” However, vendors may not bring their LISs up to specifications, especially when laboratories do not raise compliance concerns when purchasing the software.

Dr. Myers, now a clinical fellow in the Department of Pathology, Microbiology, and Immunology at Vanderbilt University Medical Center, agrees that noncompliance with the Health Insurance Portability and Accountability Act is the most troublesome finding of the study. Laboratories should be concerned about systems that don’t allow them to create unique user names and passwords for their employees, making it difficult to track user histories and employees’ access to data, he says.

Workplace practices that interfere with efficient workflow integration, such as not providing barcoding, are also problematic, says Dr. Myers, as is the systems’ inability to report test results to the target audience using the optimal formatting. Among the gaps in functionality that the survey respondents reported was the inability to use such special formatting as boldfacing, underlining, or italics to emphasize key information when transmitting results to clinicians. The respondents also identified tracking of quality control data and electronic communication of data via interfaces as areas that need to be improved.
Dr. Myers says the results confirmed many of his assumptions, but he was pleasantly surprised to find that a number of laboratories were using specialized LISs suited to molecular testing.

Since the survey was completed, he adds, specialized modules for LISs have become more widely available, replacing custom-made systems in some laboratories. “There has probably been more integration of barcodes and probably some of the reporting tools have been expanded on,” Dr. Myers says. However, the advances have come primarily in the form of these new products designed for molecular testing labs. Institutions that continue to use basic clinical or anatomic pathology systems have not seen much improvement in reporting, he notes.

Progress, in general, is likely to be slow, Dr. Carter says. Because molecular testing laboratories do not generate significant revenue, hospitals are reluctant to invest in sophisticated, expensive LISs. And laboratories using inadequate systems are likely to encounter new challenges in the era of next-generation sequencing with regard to processing large numbers of genetic variants. The lack of interoperability remains a major concern, says Dr. Carter, as many laboratories still rely on flash drives and other manual means of data transfer.

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