Whole blood gene expression profiling of neonates with confirmed bacterial sepsis.

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Changes in host gene expression in response to infection may occur in any part of the body, with the continuous interaction between blood and tissues allowing blood cells to act as biosensors for the changes. In this study we have used whole blood transcriptome profiling to systematically identify signatures and the pathway biology underlying the pathogenesis of neonatal infection. Blood samples were collected from neonates at the first clinical signs of suspected sepsis alongside age matched healthy control subjects. Here we report a detailed description of the study design, including clinical data collected, experimental methods used and data analysis workflows and which correspond with data in Gene Expression Omnibus (GEO) data sets (GSE25504). Our data set has allowed identification of a patient invariant 52-gene classifier that predicts bacterial infection with high accuracy and lays the foundation for advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis.", "claims": [{"id": "claim-method", "statement": "Per-gene hypotheses of differential expression between bacterial infection cases and control neonates were tested through linear modeling of the log2 scale expression values between groups and subsequent empirical Bayesian approaches to moderate the test statistic by pooling variance information from multiple genes (Bioconductor package ‘limma’ [4]).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484146", "locator": "sections[9] \"Data normalization and analysis\" paragraph 5", "quote": "Per-gene hypotheses of differential expression between bacterial infection cases and control neonates were tested through linear modeling of the log2 scale expression values between groups and subsequent empirical Bayesian approaches to moderate the test statistic by pooling variance information from multiple genes (Bioconductor package ‘limma’ [4])."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Deposited data are available here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25504.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484146", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data are available here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25504."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified a patient-invariant 52-gene classifier that predicts bacterial infection with high accuracy, using whole-blood transcriptome data deposited in Gene Expression Omnibus as GSE25504.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484146", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we report a detailed description of the study design, including clinical data collected, experimental methods used and data analysis workflows and which correspond with data in Gene Expression Omnibus (GEO) data sets (GSE25504)."}, {"asset": "source:pmid:26484146", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our data set has allowed identification of a patient invariant 52-gene classifier that predicts bacterial infection with high accuracy and lays the foundation for advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified a patient-invariant 52-gene classifier that predicts bacterial infection with high accuracy, using whole-blood transcriptome data deposited in Gene Expression Omnibus as GSE25504.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26484146"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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