Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.
Context.--Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun nextgeneration sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with sus...
| Publicado en: | Archives of Pathology & Laboratory Medicine Vol. 141; no. 6; pp. 776 - 787 |
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| Autores principales: | , , , , |
| Formato: | research tables/charts Journal Article |
| Publicado: |
College of American Pathologists
Jun2017
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=123400134&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 123400134 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 00039985 1FS jtl: Archives of Pathology & Laboratory Medicine issn: 00039985 maglogo: N pubinfo: dt: Jun2017 vid: 141 iid: 6 pid: 2550 pub: College of American Pathologists place: Northfield, Illinois artinfo: ui: 123400134 123400134 123400134 10.5858/arpa.2016-0539-RA 123400134 ppf: 776 ppct: 11 formats: fmt: @attributes: type: P tig: atl: Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. aug: au: Schlaberg, Robert Chiu, Charles Y. Miller, Steve Procop, Gary W. Weinstock, George affil: Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah sug: subj: Genome Infection Diagnosis Sequence Analysis Pathology Validation Studies Communicable Diseases Genetics Oncology Data Collection Data Analysis Software Biological Assay Virus Diseases Diagnosis Bacterial Infections Mycoses Polymerase Chain Reaction Medical Organizations Cerebrospinal Fluid Physiology Sensitivity and Specificity Reproducibility of Results Databases Specimen Handling ab: Context.--Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun nextgeneration sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients. Objective.--To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided. Data Sources.--Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance. Conclusions.--Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked. pubtype: Academic Journal doctype: research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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