Nanopore sequencing and its application to the study of microbial communities

Ciuffreda, Laura; Rodríguez‐Pérez, Hector; Flores, Carlos

doi:10.1016/j.csbj.2021.02.020

Cited by 121 publications

(106 citation statements)

References 152 publications

(122 reference statements)

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“…Nanopore sequencing has emerged with the potential to radically change the landscape of the -omics sciences, and researchers are still becoming acquainted to the full breadth of possibilities it offers. As the community grows, standardization and validation of wet lab protocols and computational pipelines are imperative and, while efforts in this direction have been making great strides, there is still much room for improvement (6,20).…”

Section: Discussionmentioning

confidence: 99%

“…The minION (Oxford Nanopore Technologies - ONT) is one of the latest installments of high-throughput third-generation sequencers available. This nanopore-driven device was introduced to the market in the mid 2010s, and quickly gained popularity as a tool for clinical and environmental monitoring and (meta)genomic profiling due to its capacity to generate extremely long reads while remaining highly portable and relatively cheaper than most standard sequencing technologies (5,6). Long reads are of particular importance for microbial community profiling, given that the 16S rRNA gene cannot be entirely sequenced by traditional second-generation platforms and the choice of which variable region(s) to amplify directly affects which genera can be detected with these machines (7).…”

Section: Introductionmentioning

confidence: 99%

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Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

Siqueira

Pereira-dos-Santos

Silva-Rocha³

et al. 2021

Preprint

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Fast and accurate identification of pathogens is an essential task in healthcare settings. Next generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively validated. In this work, we assess the ability of nanopore sequencing to provide reliable community profiles based on 16S rRNA sequencing in comparison to traditional Illumina platforms using samples collected from Intensive Care Units from a hospital in Brazil. While our results point that lower throughputs may be a shortcoming of the method in more complex samples, we show that the use of single-use Flongle flowcells in nanopore sequencing runs can provide insightful information on the community composition in healthcare settings.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

Siqueira

Pereira-dos-Santos

Silva-Rocha³

et al. 2021

Preprint

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“…In addition, the combination of ONT and Illumina technologies can be used to improve the quality of sequence assembly in metagenomic studies [ 93 ]. Metagenomic sequencing with MinION TM has already been used to identify fungal, bacterial, and viral pathogens on tomato and several other crops [ 94 , 95 , 96 ], and the current trend towards lower sequencing costs while improving quality suggests that direct sequencing is likely to be the next step in metagenomics [ 97 ].…”

Section: Genomicsmentioning

confidence: 99%

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

Gogolev

Ahmar

Akpınar³

et al. 2021

Plants

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The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.

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“…Nanopore Sequencing overcomes all three of the above limitations of NGS, with reads as long as the fragments that are loaded, sequencing times as short as 15 min, and Oxford Nanopore MinION instrument plus starter pack costing approximately <DOLLAR/>1000 and size of a USB drive. On the other hand, while Nanopore Sequencing has historically had a higher error rate than NGS, there has been intense recent research effort in reducing Nanopore Sequencing error rates on both the hardware [ 7 ] and software [ 8 ] sides, which has brought the raw read error rate up to a competitive level [ 7 , 9 ]. Detection of somatic single-base mutations at low variant allele frequencies (VAF) has not been demonstrated in peer reviewed publications [ 10 – 12 ].…”

Section: Introductionmentioning

confidence: 99%

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection

Thirunavukarasu¹,

Cheng

Song

et al. 2021

Genome Biol

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We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore Sequencing. OCEANS allows accurate detection of somatic mutations with VAF limits of detection between 0.05 and 1%. We construct 4 distinct multi-gene OCEANS panels targeting recurrent mutations in acute myeloid leukemia, melanoma, non-small- cell lung cancer, and hepatocellular carcinoma and validate them on clinical samples. By demonstrating detection of low VAF single nucleotide variant mutations using Nanopore Sequencing, OCEANS is poised to enable same-day clinical sequencing panels.

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Nanopore sequencing and its application to the study of microbial communities

Abstract: Graphical abstract

Cited by 121 publications

References 152 publications

Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection

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