Oxford Screening CSF and Respiratory samples ('OSCAR'): results of a pilot study to screen clinical samples from a diagnostic microbiology laboratory for viruses using Illumina next generation sequencing.

Colin SharpTanya GolubchikWilliam F GregoryAnna L McNaughtonNicholas GowMathyruban SelvaratnamAlina MireaDona FosterMonique AnderssonPaul KlenermanKatie JefferyPhilippa Clare Matthews

Published in: BMC research notes (2018)

Our data comprise a complete metagenomic dataset from 20 independent samples (10 CSF and 10 respiratory) submitted to the clinical microbiology laboratory for a large UK teaching hospital (Oxford University Hospitals NHS Foundation Trust). Sequences have been uploaded to the European Nucleotide Archive and are also presented as Krona plots through which the data can be interactively visualized. In the longer term, further optimization is required to better define sensitivity and specificity of this approach to clinical samples.

Keyphrases

healthcare
patient safety
gene expression
machine learning
copy number
cerebrospinal fluid
infectious diseases
preterm birth
antibiotic resistance genes