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- Title
End-to-End Data Automation for Pooled Sample SARS-CoV-2 Using R and Other Open-Source Tools.
- Authors
Mobini, Mahdi; Matic, Nancy; Gugten, J Grace Van Der; Ritchie, Gordon; Lowe, Christopher F; Holmes, Daniel T
- Abstract
Background: Due to supply chain shortages of reagents for real-time (RT)-PCR for SARS-CoV-2 and increasing demand on technical staff, an end-to-end data automation strategy for SARS-CoV-2 sample pooling and singleton analysis became necessary in the summer of 2020. Methods: Using entirely open source software tools—Linux, bash, R, RShiny, ShinyProxy, and Docker—we developed a modular software application stack to manage the preanalytical, analytical, and postanalytical processes for singleton and pooled testing in a 5-week time frame. Results: Pooling was operationalized for 81 days, during which time 64 pooled runs were performed for a total of 5320 sample pools and approximately 21 280 patient samples in 4:1 format. A total of 17 580 negative pooled results were released in bulk. After pooling was discontinued, the application stack was used for singleton analysis and modified to release all viral RT-PCR results from our laboratory. To date, 236 109 samples have been processed avoiding over 610 000 transcriptions. Conclusions: We present an end-to-end data automation strategy connecting 11 devices, one network attached storage, 2 Linux servers, and the laboratory information system.
- Subjects
NETWORK-attached storage; SARS-CoV-2; OPEN source software; AUTOMATION; SOFTWARE development tools; LINUX operating systems
- Publication
Journal of Applied Laboratory Medicine, 2023, Vol 8, Issue 1, p41
- ISSN
2475-7241
- Publication type
Article
- DOI
10.1093/jalm/jfac109