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Diagnosis of childhood bacterial and viral infection using host RNA expression

ABSTRACT: Diagnosis of childhood bacterial and viral infection using host RNA expression

PROVIDER: PRJNA295175 | ENA |

REPOSITORIES: ENA

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Diagnosis of childhood bacterial and viral infection using host RNA expression [Discovery set]

Project description:Genome-wide analysis of transcriptional profiles in children <17 years of age with bacterial or viral infections or with clinical features suggestive of infection.

2016-08-29 | GSE72809 | GEO

Diagnosis of childhood bacterial and viral infection using host RNA expression [validation set]

Project description:Genome-wide analysis of transcriptional profiles in children <17 years of age with bacterial or viral infections or with clinical features suggestive of infection.

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Diagnosis of childhood bacterial and viral infection using host RNA expression

Project description:This SuperSeries is composed of the SubSeries listed below.

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Host Gene Expression in Nasal and Blood Samples for the Diagnosis of Viral Respiratory Infection

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A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants

Project description:The continued emergence of SARS-CoV-2 variants is one of several factors that may cause false negative viral PCR test results. Such tests are also susceptible to false positive results due to trace contamination from high viral titer samples. Host immune response markers provide an orthogonal indication of infection that can mitigate these concerns when combined with direct viral detection. Here, we leverage nasopharyngeal swab RNA-seq data from patients with COVID-19, other viral acute respiratory illnesses and non-viral conditions (n=318) to develop support vector machine classifiers that rely on a parsimonious 2-gene host signature to diagnose COVID-19. We find that optimal classifiers include an interferon-stimulated gene that is strongly induced in COVID-19 compared with non-viral conditions, such as IFI6, and a second immune-response gene that is more strongly induced in other viral infections, such as GBP5. The IFI6+GBP5 classifier achieves an area under the receiver operating characteristic curve (AUC) greater than 0.9 when evaluated on an independent RNA-seq cohort (n=553). We further provide proof-of-concept demonstration that the classifier can be implemented in a clinically relevant RT-qPCR assay. Finally, we show that its performance is robust across common SARS-CoV-2 variants and is unaffected by cross-contamination, demonstrating its utility for improving accuracy of COVID-19 diagnostics.

2021-11-15 | GSE188678 | GEO

A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants

Project description:A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants

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A 5-transcript signature for discriminating viral and bacterial etiology in pediatric pneumonia

Project description:Pneumonia stands as the primary cause of death among children under five, with its onset attributed to a broad spectrum of microorganisms. Diagnosis poses an ongoing challenge, relying on clinical or microbiological criteria, often resulting in delayed and inaccurate treatment and unnecessary therapy. Our research focuses on identifying host transcriptomic biomarkers in the blood of children affected by viral and bacterial pneumonia, alongside healthy controls. The main goal is to establish a gene-expression signature enhancing disease diagnosis and management. We conducted an analysis of a total of 192 whole blood samples, comprising 38 controls and 154 viral and bacterial pneumonia patients recruited through the EUCLIDS clinical network. Our investigation identified 5,486 differentially expressed genes (DEGs) when comparing blood RNA from pneumonia patients with healthy controls. Functional enrichment analysis highlighted pathways related to the immune system response, encompassing neutrophil degranulation, humoral immune response, and various inflammatory pathways. In the comparative analysis of gene expression between viral and bacterial pneumonia patients, we identified 272 DEGs. Gene set analysis revealed a significant difference in pathway enrichment for the immune response, contingent on the over-regulation of gene sets in viral or bacterial pneumonias. Furthermore, we identified a 5-transcript host signature specifically designed to distinguish between viral and bacterial pediatric pneumonia (FAM20A, BAG3, TDRD9, MXRA7 and KLF14; AUC: 0.95 [0.88–1.00]), pseudo-validated in a cohort including probable bacterial and viral patients (AUC: 0.87 [0.77–0.97]). This signature holds the potential to enhance the accuracy of previously described general transcript-based signatures for viral and bacterial infections.

2024-12-09 | GSE261482 | GEO

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