LOMT - Laboratory Optimizer for Mass Testing
Scaling up COVID-19 testing
Improving the performance of medical laboratories and reducing the cost and time of testing
Laboratory Optimizer for Mass Testing (LOMT) is open source software for the management of COVID-19 pool testing. It allows the testing of 2 to 30 times more people with the existing resources of a laboratory by reducing the quantity of assays, reagents and time spent on each test.
- Qualitative test of the presence of a single target component — i.e., SARS-CoV-2 RNA
- PCR and other techniques that allow mixing several specimens into an assay
- A large number of single-type tests (>100) with a prevalence below 20%
- Frequent screening of high-risk groups or those involved in human interaction activities — medical staff, teachers and students, public services, company employees
- Epidemiological surveillance of the population to monitor the general infectious state, early detection of infected people and localization of foci of infection
In the pool-testing method, the analysis process of a laboratory remains the same as in standard individual testing. The difference concerns only the analyte; instead of analyzing an individual specimen, a mixture of several specimens — a pool — is analyzed.
The program is a tool for laboratory personnel. It designs the specimen mixing plan, tracks specimens and assays, and decodes the results of assays completed into the results of specimens.
LOMT supports several pool-testing algorithms and strategies, from plain grouping of samples into pools to more complex algorithms with binary search, combinatorial analysis and probability analysis, and it suggests the optimal strategies depending on the prevalence, optimization task and operational constraints.
The program offers a user-friendly visual guide for manual specimen pipetting and result reporting, and can be integrated with the laboratory information system and laboratory robotics.
How it works
The task is to analyze a batch of swabs and detect rare positive swabs with the minimum quantity of assays spent or minimal time to obtain results for the full batch.
A laboratory assistant enters into the program the parameters of a batch of swabs and goes through a visual interface that guides pipetting and mixing of specimens into pools. The program splits specimens into several groups; the specimens from each group are mixed into a pool and tested with a single assay. The results of the assays are submitted to the program by laboratory assistant or automatically imported from a LIS/LIMS. The program decodes the results: it reports all definitely identified negative and positive specimens, and plans the next stage of pooling and analysis for the remaining specimens.
The mixing, analysis, and decoding steps continue until all the samples have been identified as negative or positive.
The major indicator of the efficiency of a pool-testing strategy is the reduction of the number of assays for a certain number of specimens. The analysis process takes a long time, consumes reagents and requires significant manual labor. Other related processes require much less time and cost, and in most cases, a tenfold reduction in the number of assays increases the throughput of the laboratory by 9 times and also decreases the cost of the testing of one person by 9 times.
The number of assays primarily depends on prevalence (the proportion of positives samples) and the maximum pool size (the limit of dilution of a specimen). The lower the prevalence, the larger the pool size that can be used, and ultimately, fewer assays will be required. For example, for 1% prevalence, the maximal effective pool size is 69, for 10% prevalence it is 7 and for prevalence above 25% the pool size becomes less than 4 and the efficiency becomes too low to be worth using.
Different laboratories can operate with different values of prevalence, constraints of testing and priorities of optimization, and these values can change over time. LOMT supports several different pooling strategies and automatically searches for the optimal strategy for every specific condition.
For a high prevalence (10%) and the maximum pool size 8, the maximum reduction of the number of assays is 2.1x compared to the individual testing: for a batch of 1000 specimens the pool testing uses 477 assays on average, while the individual testing uses 1000 assays. For a medium prevalence (1%) and the maximum pool size 32, the maximum reduction of the number of assays is 11x, with 90 assays on avarage for a batch of 1000 specimens. For a low prevalence (0.1%) and the maximum pool size 32, the maximum reduction of the number of assays is 25x, with 39 assays on average for a batch of 1000 specimens.
More information is available in “The brief comparison of the operational efficiency of pool-testing strategies for COVID-19 mass testing in PCR laboratories.”
LOMT is implemented as a cloud application with a graphical user interface running on a web browser without installation on any desktop computer, laptop or tablet. It can be also installed in a laboratory or within the IT infrastructure of an enterprise for large-scale deployment.
LOMT is also available as an API service that can be used in software developed by LIS/LIMS vendors and laboratory equipment vendors. The service can be accessed by HTTPS/JSON over the Internet or virtual private networks in major public clouds.
LOMT Pool Testing now available at Amazon Web Services
LOMT Pool Testing now available at Microsoft Azure
A study on the operational efficiency of pool-testing strategies
Release 0.9.5: An automated search for the optimial pooling strategy for an estimated prevalence
Release 0.9: A visual mixing guide optimized for tablet and laptop/transformer devices
Release 0.8: User interface improvements in the samples mixing workflow
Release 0.6: A GUI cloud app
Release 0.3: Specimens, assays, and alogrithm management library, command line interface
- Facilitating Diagnostic Test Availability for Asymptomatic Testing and Sample Pooling — FDA, 2020-06-16
- Evaluation of COVID-19 RT-qPCR test in multi-sample pools — Oxford University Press, 2020-05-02
- Pooling of samples for testing for SARS-CoV-2 in asymptomatic people — The Lancet, 2020-04-28
- Efficient and Practical Sample Pooling for High-Throughput PCR Diagnosis of COVID-19 — medRxiv, 2020-04-14
- Pooling nasopharyngeal/throat swab specimens to increase testing capacity for influenza viruses by PCR — Journal of Clinical Microbiology, 2012
- Group testing — Wikipedia
- COVID-19 testing — Wikipedia
- Mass screening to halt COVID-19