A modular framework for the development of targeted Covid-19 blood transcript profiling panels
Autor: | Ricardo Garcia Branco, Damien Chaussabel, Andrea De Maria, Alberto Ballestrero, Matteo Bassetti, Davide Bedognetti, Tobias Brummaier, Mathieu Garand, Gabriele Zoppoli, Basirudeen Syed Ahamed Kabeer, Nicole Baldwin, Matthew C. Altman, Benjamin Tang, Zohreh Tatari-Calderone, Mohammed Toufiq, Darawan Rinchai, Sara Deola, Mohamed Alfaki |
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Jazyk: | angličtina |
Rok vydání: | 2020 |
Předmět: |
Adult
0301 basic medicine Coronavirus disease 2019 (COVID-19) Blood transcriptomics Covid-19 Immune monitoring SARS-CoV-2 Antibodies Viral Betacoronavirus Coronavirus Infections Gene Expression Profiling Humans Immune System Internet Pandemics Pneumonia Viral RNA-Seq Software Transcriptome Computer science Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lcsh:Medicine Transcript profiling Computational biology Antibodies General Biochemistry Genetics and Molecular Biology Immune profiling 03 medical and health sciences 0302 clinical medicine Immune system Profiling (information science) Viral business.industry Research lcsh:R COVID-19 Pneumonia General Medicine Modular design Gene expression profiling Coronavirus 030104 developmental biology 030220 oncology & carcinogenesis business |
Zdroj: | Journal of Translational Medicine, Vol 18, Iss 1, Pp 1-23 (2020) Journal of Translational Medicine |
Popis: | Background Covid-19 morbidity and mortality are associated with a dysregulated immune response. Tools are needed to enhance existing immune profiling capabilities in affected patients. Here we aimed to develop an approach to support the design of targeted blood transcriptome panels for profiling the immune response to SARS-CoV-2 infection. Methods We designed a pool of candidates based on a pre-existing and well-characterized repertoire of blood transcriptional modules. Available Covid-19 blood transcriptome data was also used to guide this process. Further selection steps relied on expert curation. Additionally, we developed several custom web applications to support the evaluation of candidates. Results As a proof of principle, we designed three targeted blood transcript panels, each with a different translational connotation: immunological relevance, therapeutic development relevance and SARS biology relevance. Conclusion Altogether the work presented here may contribute to the future expansion of immune profiling capabilities via targeted profiling of blood transcript abundance in Covid-19 patients. |
Databáze: | OpenAIRE |
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