MinION as part of a biomedical rapidly deployable laboratory

Walter, Mathias C.; Zwirglmaier, Katrin; Vette, Philipp; Holowachuk, Scott A.; Stoecker, Kilian; Genzel, Gelimer H.; Antwerpen, Markus

doi:10.1016/j.jbiotec.2016.12.006

Cited by 46 publications

(29 citation statements)

References 27 publications

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“…The Oxford Nanopore MinION is a portable sequencing device that has recently emerged as a rapid and cost-effective sequencing platform that produces long reads, and has multiple applications in clinical microbiology, such as pathogen detection [36], bacterial genome assembly [37] and plasmid and resistance gene detection [38,39]. Specific to microbiome analysis, the utility of the MinION platform has been demonstrated in rRNA amplicon-based sequencing [40][41][42] and in metagenomics for outbreak analysis of bacteria [43] and viruses [44].…”

Section: Discussionmentioning

confidence: 99%

MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing

Taylor

Pearson

Miller

et al. 2019

Preprint

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Recent evidence suggests a role for the gut microbiome in the development and progression of colorectal cancer. In this study we compare MinION sequencing with meta-transcriptomics and amplicon-based sequencing for microbiome analysis of colorectal tumour tissue samples. DNA and RNA were extracted from 11 colorectal tumour samples. RNA-Sequencing, 16S rRNA amplicon sequencing and MinION genomic sequencing was carried out and resulting data used as input for taxonomic classification using Kraken2. Taxonomic concordance between the three platforms at different taxonomic levels was tested on a per sample basis. The average number of reads per sample using RNA-Sequencing was more than 129 times that generated using MinION sequencing. However, the average read length of MinION sequences was more than 13 times that of RNA or 16S rRNA amplicon sequencing. 16S sequencing was less informative beyond the genus level, and both RNA-Sequencing and MinION sequencing could detect more phyla and genera in the same samples, compared to 16S sequencing. Long-read sequences generated using MinION sequencing can compensate for low numbers of reads for bacterial classification. MinION sequencing can discriminate between bacterial strains and plasmids and shows potential as a tool for microbiome sequencing of colorectal cancers in a clinical setting.

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Section: Discussionmentioning

confidence: 99%

MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing

Taylor

Pearson

Miller

et al. 2019

Preprint

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“…Previously, countries could control the physical export of samples to ensure that there was agreement on how samples could be used. With the advent of portable sequencing devices that can be used in the field [45][46][47][48][49] and gene synthesis technologies it is now possible to design and produce a new vaccine starting with only sequence data, without physical transfer of material.…”

Section: Outstanding Challengesmentioning

confidence: 99%

UK vaccines network: Mapping priority pathogens of epidemic potential and vaccine pipeline developments

Noad¹,

Simpson²,

Fooks³

et al. 2019

Vaccine

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a b s t r a c tDuring the 2013-2016 Ebola outbreak in West Africa an expert panel was established on the instructions of the UK Prime Minister to identify priority pathogens for outbreak diseases that had the potential to cause future epidemics. A total of 13 priority pathogens were identified, which led to the prioritisation of spending in emerging diseases vaccine research and development from the UK. This meeting report summarises the process used to develop the UK pathogen priority list, compares it to lists generated by other organisations (World Health Organisation, National Institutes of Allergy and Infectious Diseases) and summarises clinical progress towards the development of vaccines against priority diseases. There is clear technical progress towards the development of vaccines. However, the availability of these vaccines will be dependent on sustained funding for clinical trials and the preparation of clinically acceptable manufactured material during inter-epidemic periods.

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“…As technology continues to advance, the linkages of genomics and precision medicine with emerging infectious diseases will continue to strengthen. Improvements with sequencing accuracy and speed are pushing pathogen-specific genomics to near real-time [73,74], allowing rapid access to critical information within a timeframe that can impact an outbreak response [44,45]. Confidence in the results from sequencing is leading to clinically actionable diagnostic patient testing [29], and it is reasonable to foresee rapid, pathogen agnostic diagnostic assays routinely utilized in the clinic.…”

Section: Closing Remarksmentioning

confidence: 99%