Laboratory information system requirements to manage the COVID-19 pandemic: A report from the Belgian national reference testing center

Posted on August 25, 2020 By LabLynx Journal articles

Though the COVID-19 pandemic has been in force for months, seemingly little has been published (even ahead of print) in academic journals of the technological challenges of managing the growing mountain of research and clinical diagnostic data. Weemaes et al. are one of the exceptions, with this pre-print June publication in the Journal of the American Medical Informatics Association. The authors, from Belgium's University Hospitals Leuven, present their approach to rapidly expanding their laboratory's laboratory information system (LIS) to address the sudden workflow bottlenecks associated with COVID-19 testing. They describe how using a change management framework to rapidly drive them forward, the authors were able "to streamline sample ordering through a CPOE system, and streamline reporting by developing a database with contact details of all laboratories in Belgium," while improving epidemiological reporting and exploratory data mining of the data for scientific research. They also address the element of "meaningful use" of their LIS, which often gets overlooked.

Comprehensive analyses of SARS-CoV-2 transmission in a public health virology laboratory

Posted on August 18, 2020 By LabLynx Journal articles

With COVID-19, we think of small outbreaks occurring from humans being in close proximity at restaurants, parties, and other events. But what about laboratories? Zuckerman et al. share their tale of a small COVID-19 outbreak at Israel’s Central Virology Laboratory (ICVL) in mid-March 2020 and how they used their lab tech to determine the transmission sources. With eight known individuals testing positive for the SARS-CoV-2 virus overall, the researchers walk step by step through their quarantine and testing processes to "elucidate person-to-person transmission events, map individual and common mutations, and examine suspicions regarding contaminated surfaces." Their analyses found person-to-person contact—not contaminated surface contact—was the transmission path. They conclude that their overall analysis verifies the value of molecular testing and capturing complete viral genomes towards determining transmission vectors "and confirms that the strict safety regulations observed in ICVL most likely prevented further spread of the virus."

Extending an open-source tool to measure data quality: Case report on Observational Health Data Science and Informatics (OHDSI)

Posted on August 11, 2020 By LabLynx Journal articles

In this 2020 short report from Dixon et al., lessons learned from attempts to expand data quality measures in the open-source tool Observational Health Data Science and Informatics (OHDSI) are presented. Noting a lack of data quality assessment and improvement mechanisms in health information systems in general, the researchers sought to improve OHDSI for public health surveillance use cases. After explaining the practical uses of OHDSI, the authors state their case for why measuring completeness, timeliness, and information entropy within OHDSI would be useful. Though not getting approval to add timeliness to the system, they conclude that high value remains "in adapting existing infrastructure and tools to support expanded use cases rather than to just create independent tools for use by a niche group."