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
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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