Report
A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays
| العنوان: | A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays |
|---|---|
| المؤلفون: | Li, Po-E, Gutiérrez, Adán Myers y, Davenport, Karen, Flynn, Mark, Hu, Bin, Lo, Chien-Chi, Jackson, Elais Player, Shakya, Migun, Xu, Yan, Gans, Jason, Chain, Patrick S. G. |
| سنة النشر: | 2020 |
| المجموعة: | Quantitative Biology |
| مصطلحات موضوعية: | Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods |
| الوصف: | Summary: Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true positive rate (recall) to simplify assay comparisons. Availability: https://covid19.edgebioinformatics.org/#/assayValidation. Contact: Jason Gans (jgans@lanl.gov) and Patrick Chain (pchain@lanl.gov) Comment: Application Note. Main: 2 pages, 1 figure. Supplementary: 6 pages, 8 figures, 1 table. Total: 8 pages, 9 figures, 1 table. Application url: https://covid19.edgebioinformatics.org/#/assayValidation Contact: Jason Gans (jgans@lanl.gov) and Patrick Chain (pchain@lanl.gov) Submitted to: Bioinformatics |
| نوع الوثيقة: | Working Paper |
| URL الوصول: | http://arxiv.org/abs/2006.04566 |
| رقم الانضمام: | edsarx.2006.04566 |
| قاعدة البيانات: | arXiv |
| الوصف غير متاح. |