The potential of whole genome NGS for infectious disease diagnosis

Lecuit, Marc; Éloit, Marc

doi:10.1586/14737159.2015.1111140

Cited by 49 publications

(33 citation statements)

References 17 publications

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“…Application of MSS to diagnostic virology has great appeal based on the capability for (i) broad-range detection and (ii) detailed taxonomic characterization (40)(41)(42)(43)(44)(45)(46)(47) and for characterization of antiviral resistance genotypes (48). Our findings in this study illustrate and quantitate these advantages using actual clinical samples and measure the further enhancement achieved by the use of targeted sequence capture to improve the sensitivity of standard metagenomic shotgun sequencing.…”

Section: Discussionmentioning

confidence: 99%

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

Wylie

Buller

et al. 2018

J Clin Microbiol

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Metagenomic shotgun sequencing (MSS) is a revolutionary approach to viral diagnostic testing that allows simultaneous detection of a broad range of viruses, detailed taxonomic assignment, and detection of mutations associated with antiviral drug resistance. To enhance sensitivity for virus detection, we previously developed ViroCap, a targeted sequence capture panel designed to enrich nucleic acid from a comprehensive set of eukaryotic viruses prior to sequencing. To demonstrate the utility of MSS with targeted sequence capture for detecting clinically important viruses and characterizing clinically important viral features, we used ViroCap to analyze clinical samples from a diagnostic virology laboratory containing a broad range of medically relevant viruses. From 26 samples, MSS with ViroCap detected all of the expected viruses and 30 additional viruses. Comparing sequencing after capture enrichment with standard MSS, we detected 13 viruses only with capture enrichment and observed a consistent increase in the number and percentage of viral sequence reads as well as the breadth and depth of coverage of the viral genomes. Compared with clinical testing, MSS enhanced taxonomic assignment for 15 viruses, and codons associated with antiviral drug resistance in influenza A virus, herpes simplex virus (HSV), human immunodeficiency virus (HIV), and hepatitis C virus (HCV) could be analyzed. Overall, in clinical samples, MSS with targeted sequence capture provides enhanced virus detection and information of clinical and epidemiologic relevance compared with clinical testing and MSS without targeted sequence capture.

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Section: Discussionmentioning

confidence: 99%

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

Wylie

Buller

et al. 2018

J Clin Microbiol

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“…The arrival of next-generation sequencing (NGS) technologies offers for the first time an opportunity to locate these mutations. NGS technology has advanced at an exponential pace, with the cost per megabase of sequence halving regularly 4 5 . This has enabled enhanced diagnosis for both genetic and infectious diseases 6 , as well as providing insights into mutations driving tumorigenesis.…”

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confidence: 99%

Panel-Based Population Next-Generation Sequencing for Inherited Retinal Degenerations

Carrigan

Duignan

Malone

et al. 2016

Sci Rep

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Inherited retinopathies affect approximately two and a half million people globally, yet the majority of affected patients lack clear genetic diagnoses given the diverse range of genes and mutations implicated in these conditions. We present results from a next-generation sequencing study of a large inherited retinal disease patient population, with the goal of providing clear and actionable genetic diagnoses. Targeted sequencing was performed on 539 individuals from 309 inherited retinal disease pedigrees. Causative mutations were identified in the majority (57%, 176/309) of pedigrees. We report the association of many previously unreported variants with retinal disease, as well as new disease phenotypes associated with known genes, including the first association of the SLC24A1 gene with retinitis pigmentosa. Population statistics reporting the genes most commonly implicated in retinal disease in the cohort are presented, as are some diagnostic conundrums that can arise during such studies. Inherited retinal diseases represent an exemplar group of disorders for the application of panel-based next-generation sequencing as an effective tool for detection of causative mutations.

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“…Biodiversity [7] Disease diagnostics [8] Nutrition [9] Environment [10] Aging disease [11] Forensic biology [12] Agriculture Table 1. The application of NGS in biotechnology.…”

Section: Application Referencesmentioning

confidence: 99%

Explore the Novel Biomarkers through Next-Generation Sequencing

2018

Genotyping

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Next-generation sequencing is being a robust technology for the practice of clinical diagnosis. The reason is that this technology offers the advantage of higher sensitivity and the potential to detect the full genome sequence of pathogens, including unknown pathogen species. In view of the exceptional advantages of next-generation sequencing, the technology can be used to improve and revolutionize conventional pathogenic detection methodologies. The technological result holds great possibilities in helping to support clinicians with richer insights into host's genomic features, including the appropriateness to drug resistance based on the sequencing mapping of the microorganism. Besides, the technology will help discover the source of infection and insights into treatment directions, furthermore lead to the advancements in diagnosis. Eventually, this technology will benefit the clinical community in infectious disease prediction and prevention.

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The potential of whole genome NGS for infectious disease diagnosis

Cited by 49 publications

References 17 publications

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

Panel-Based Population Next-Generation Sequencing for Inherited Retinal Degenerations

Explore the Novel Biomarkers through Next-Generation Sequencing

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