Laboratory Optimizer for Mass Testing (LOMT) is open source software for the management of pool testing workflows. 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.
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.
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.
| Prevalence | Specimens | Pool size | Assays | Reduction |
|---|---|---|---|---|
| 10% | 1000 | 8 | 477 | 2.1 |
| 1% | 1000 | 32 | 90 | 11.1 |
| 0.1% | 1000 | 32 | 39 | 25.6 |
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.
The program is also available at Microsoft Azure and Amazon Web Services.
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.
European Open Science Cloud. EOSCSecretariat COVID-19 Fast Track Funding, request 233 – EOSCsecretariat.eu has received funding from the European Union’s Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644
