About: Challenges of the Unknown: Clinical Application of Microbial Metagenomics

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Challenges of the Unknown: Clinical Application of Microbial Metagenomics
Creator	Anscombe, Catherine Gharbia, Saheer Rose, Graham Mee, Edward Misra, Raju Wooldridge, David
Source	Medline; PMC
abstract	Availability of fast, high throughput and low cost whole genome sequencing holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events to understanding the role played by microbial communities in health and disease. Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge. As proof of principle, we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological model using benchtop technology. The datasets were then analysed using a bioinformatic pipeline developed around recent fast classification methods. A targeted approach was able to detect 20 of the viruses against a background of host contamination from multiple sources and bacterial contamination. An alternative untargeted identification method was highly correlated with these classifications, and over 1,600 species were identified when applied to the complex biological model, including several species captured at over 50% genome coverage. In summary, this study demonstrates the great potential of applying metagenomics within the clinical laboratory setting and that this can be achieved using infrastructure available to nondedicated sequencing centres.
has issue date	2015-09-14(xsd:dateTime)
bibo:doi	10.1155/2015/292950
bibo:pmid	26451363
has license	cc-by
sha1sum (hex)	daeba3efafc5b3f9e71e38069aadf1e0178bac9d
schema:url	https://doi.org/10.1155/2015/292950
resource representing a document's title	Challenges of the Unknown: Clinical Application of Microbial Metagenomics
has PubMed Central identifier	PMC4584244
has PubMed identifier	26451363
schema:publication	Int J Genomics
resource representing a document's body	covid:daeba3efafc5b3f9e71e38069aadf1e0178bac9d#body_text
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