RNA-Sequencing of whole blood samples from children with a range of acute febrile illnesses
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-MTAB-11671 | biostudies-arrayexpress |
SECONDARY ACCESSION(S): ERP142716
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The cohort comprised patients recruited between Sept 2014- June 2020. It includes patients with bacteremia and positive viral diagnostic test in the context of acute admission. All patients with definite infection were used for signature discovery. Whole blood was collected at the time of recruitment in Tempus Blood RNA tubes and total RNA was isolated with the Tempus Spin RNA Isolation Kit (ThermoFisher Scientific) according to the manufacturer’s instructions. RNA samples were stored at −80 °C until further analysis. After additional DNAse treatment, library preparation and sequencing of 30 million 150bp, paired end reads were conducted using the Illumina's TruSeq® RNA Sample Preparation Kit; ribosomal and globin RNA depletion was performed using the Illumina Ribo-Zero Gold kit and HiSeq 4000 at The Wellcome Centre for Human Genetics in Oxford UK.
2024-09-23 | E-MTAB-13307 | biostudies-arrayexpress
Project description:The cohort comprised patients recruited between August 2014 - April 2017. It includes patients with bacteremia, positive viral diagnostic test in the context of acute admission and those with no positive microbial diagnostic test, no infection-related ICD-10 diagnostic codes, and no empirical antiviral/antimicrobial treatment >48hrs duration. RNA was subjected to RNA-Sequencing. All patients with definite bacterial or viral infection were used for gene signature discovery. Whole blood was collected at the time of recruitment in Tempus Blood RNA tubes and total RNA was isolated with the TempusTM Spin RNA Isolation Kit (ThermoFisher Scientific) according to the manufacturer’s instructions. RNA samples were stored at −80 °C until further analysis. After additional DNAse treatment, library preparation and sequencing of 30 million 100bp, paired end reads were conducted using the Illumina's TruSeq® RNA Sample Preparation Kit; ribosomal and globin RNA depletion was performed using the Illumina Ribo-Zero Gold kit and HiSeq 4000 at The Wellcome Centre for Human Genetics in Oxford UK.
2021-08-11 | E-MTAB-10527 | biostudies-arrayexpress
Project description:Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA-Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups.
2022-07-19 | E-MTAB-10926 | biostudies-arrayexpress
Project description:Multisystem inflammatory syndrome in children (MIS-C) occurs in some children approximately 2-6 weeks following infection with SARS-CoV-2. Clinical symptoms are highly overlapping with Kawasaki disease (KD) and bacterial (DB) and viral (DV) infections, making diagnosis particularly challenging. Host whole blood transcriptomics can reveal specific combinations of host genes whose expression patterns can distinguish between disease groups of interest. We performed whole blood RNA-Sequencing of individuals with MIS-C, KD, bacterial and viral infections to identify a number of host genes that, when combined, could be used to diagnose MIS-C. This data contains processed data only. Raw data will be available via a controlled access archive.
2023-06-27 | E-MTAB-12793 | biostudies-arrayexpress
Project description:ABSTRACT Background. Acute Kawasaki disease (KD) is difficult to distinguish from other acute rash/fever illnesses, in part because the etiologic agent(s) and pathophysiology remain poorly characterized. As a result, diagnosis and critical therapies may be delayed. Methods. We used DNA microarrays to identify possible diagnostic features of KD. We compared gene expression patterns in the blood of 23 children with acute KD and 18 age-matched febrile children with three illnesses that resemble KD. Results. Genes associated with platelet and neutrophil activation were expressed at higher levels in KD patients than in patients with acute adenovirus infections or systemic adverse drug reactions but not in patients with scarlet fever; genes associated with B cell activation were also expressed at higher levels in KD patients than in controls. A striking absence of interferon-stimulated gene expression in the KD patients was confirmed in an independent cohort of KD subjects. We successfully predicted the diagnosis in 21 of 23 KD patients and 7 of 8 adenovirus patients using a set of 38 gene transcripts. Conclusions. These findings provide insight into the molecular features that distinguish KD from other febrile illnesses, and support the feasibility of developing novel diagnostic reagents for KD based on the host response. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Disease State: One of Kawasaki Disease (KD) or control (C) of Scarlet fever (C-sf), adenovirus infection (C-ai) or drug reaction (C-dr) disease_state_design
2010-06-24 | E-GEOD-15297 | biostudies-arrayexpress
Project description:ABSTRACT Background. Acute Kawasaki disease (KD) is difficult to distinguish from other acute rash/fever illnesses, in part because the etiologic agent(s) and pathophysiology remain poorly characterized. As a result, diagnosis and critical therapies may be delayed. Methods. We used DNA microarrays to identify possible diagnostic features of KD. We compared gene expression patterns in the blood of 23 children with acute KD and 18 age-matched febrile children with three illnesses that resemble KD. Results. Genes associated with platelet and neutrophil activation were expressed at higher levels in KD patients than in patients with acute adenovirus infections or systemic adverse drug reactions but not in patients with scarlet fever; genes associated with B cell activation were also expressed at higher levels in KD patients than in controls. A striking absence of interferon-stimulated gene expression in the KD patients was confirmed in an independent cohort of KD subjects. We successfully predicted the diagnosis in 21 of 23 KD patients and 7 of 8 adenovirus patients using a set of 38 gene transcripts. Conclusions. These findings provide insight into the molecular features that distinguish KD from other febrile illnesses, and support the feasibility of developing novel diagnostic reagents for KD based on the host response. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Disease State: One of Kawasaki Disease (KD) or control (C) of Scarlet fever (C-sf), adenovirus infection (C-ai) or drug reaction (C-dr)
2009-08-12 | GSE15297 | GEO
Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip
2011-12-31 | GSE28142 | GEO
Project description:Whole blood transcriptional profiles of patients with (1) active pulmonary ['AdjuVIT active TB' and 'New active pulmonary'] and (2) extrapulmonary TB ['New active-extrapulmonary'] at time of diagnosis, (3) long-term recovery after treatment for active pulmonary TB ['AdjuVIT active TB'], (4) febrile illnesses presenting to hospital ['Fever mixed infection'] and (5) febrile pneumonia ['Fever pneumonia'] before antibiotic treatment, and (6) healthy vounteers. Each array sample represents a separate individual in each group. This submission includes two human whole genome Agilent Array Designs: A-MEXP-2104 and A-AGIL-28. Each of the individual raw array files are included as well as a single processed file representing the data matrix of all the merged and normalised data for the probes that are shared by the two array designs.
2016-10-28 | E-MTAB-4257 | biostudies-arrayexpress
Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip From each serum sample, total nucleic acid was extracted and used to prepare a randomly-primed dsDNA library. These libraries were fluorescently labeled and hybrized to Virochip arrays.
2011-12-31 | E-GEOD-28142 | biostudies-arrayexpress
Project description:Background: Non-malaria febrile illnesses such as bacterial bloodstream infections (BSI) are a leading cause of disease and mortality in the tropics. However, there are no reliable, simple diagnostic tests for identifying BSI or other severe non-malaria febrile illnesses. We hypothesized that different infectious agents responsible for severe febrile illness would impact on the host metabololome in different ways, and investigated the potential of plasma metabolites for diagnosis of non-malaria febrile illness. </p> Methodology: We conducted a comprehensive mass-spectrometry based metabolomics analysis of the plasma of 61 children with severe febrile illness from a malaria-endemic rural African setting. Metabolite features characteristic for non-malaria febrile illness, BSI, severe anemia and poor clinical outcome were identified by receiver operating curve analysis. </p> Principal Findings: The plasma metabolome profile of malaria and non-malaria patients revealed fundamental differences in host response, including a differential activation of the hypothalamic-pituitary-adrenal axis. A simple corticosteroid signature was a good classifier of severe malaria and non-malaria febrile patients (AUC 0.82, 95% CI: 0.70-0.93). Patients with BSI were characterized by upregulated plasma bile metabolites; a signature of two bile metabolites was estimated to have a sensitivity of 98.1% (95% CI: 80.2-100) and a specificity of 82.9% (95% CI: 54.7-99.9) to detect BSI in children younger than 5 years. This BSI signature demonstrates that host metabolites can have a superior diagnostic sensitivity compared to pathogen-detecting tests to identify infections characterized by low pathogen load such as BSI. </p> Conclusions: This study demonstrates the potential use of plasma metabolites to identify causality in children with severe febrile illness in malaria-endemic settings.
2016-03-17 | MTBLS315 | MetaboLights