MinION rapid sequencing: Review of potential applications in neurosurgery

Patel, Arpan; Belykh, Evgenii; Miller, Eric J; George, Laeth; Martirosyan, Nikolay L.; Byvaltsev, Vadim A.; Preul, Mark C.

doi:10.4103/sni.sni_55_18

Cited by 22 publications

(5 citation statements)

References 65 publications

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“…A promising approach for possible use in routine diagnostics is the sequencing by Nanopore device (Nanoporetech, Oxford, England). This approach provides long reads thus analyzing structural variants, point mutations, bisulfite‐free methylation and epitranscriptome profiles, using a single device with affordable capital cost 95 . Intriguingly, this method has been also proposed for potential intraoperatorial diagnosis.…”

Section: Technical Approaches To Investigate Epigenetic Biomarkers In...mentioning

confidence: 99%

Epigenetic alterations in glioblastomas: Diagnostic, prognostic and therapeutic relevance

Montella¹,

Cuomo

Gaudio

et al. 2022

Intl Journal of Cancer

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Glioblastoma, the most common and heterogeneous tumor affecting brain parenchyma, is dismally characterized by a very poor prognosis. Thus, the search of new, more effective treatments is a vital need. Here, we will review the druggable epigenetic features of glioblastomas that are, indeed, currently explored in preclinical studies and in clinical trials for the development of more effective, personalized treatments. In detail, we will review the studies that have led to the identification of epigenetic signatures, IDH mutations, MGMT gene methylation, histone modification alterations, H3K27 mutations and epitranscriptome landscapes of glioblastomas, in each case discussing the corresponding targeted therapies and their potential efficacy. Finally, we will emphasize how recent technological improvements permit to routinely investigate many glioblastoma epigenetic biomarkers in clinical practice, further enforcing the hope that personalized drugs, targeting specific epigenetic features, could be in future a therapeutic option for selected patients.

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Section: Technical Approaches To Investigate Epigenetic Biomarkers In...mentioning

confidence: 99%

Epigenetic alterations in glioblastomas: Diagnostic, prognostic and therapeutic relevance

Montella¹,

Cuomo

Gaudio

et al. 2022

Intl Journal of Cancer

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“…Next generation sequencing (NGS) platforms have been evolving for the last decade, from early short read length platforms (e.g., 454 'tag' pyrosequencing or Ion Torrent technologies) to current short read Ilumina platforms (Hiseq, Miseq, Miniseq). Emerging long read length technologies such as Nanopore sequencing (e.g., Oxford MinION) or by Pacific Biosciences hold promise for even more information dense sequencing (see reviews of NGS sequencing, Goodwin et al, 2016;Patel et al, 2018;Mantere et al, 2019). NGS technologies produce so much data per sample that the problem has moved from the high expense of sequencing to the expense of hiring personnel to process hundreds of gigabytes of data.…”

Section: Changing Previous Assumptions Using Modern Techniques -A 'Second Revolution' In Molecular Microbiologymentioning

confidence: 99%

A Review of Landfill Microbiology and Ecology: A Call for Modernization With ‘Next Generation’ Technology

2020

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Engineered and monitored sanitary landfills have been widespread in the United States since the passage of the Clean Water Act (1972) with additional controls under RCRA Subtitle D (1991) and the Clean Air Act Amendments (1996). Concurrently, many common perceptions regarding landfill biogeochemical and microbiological processes and estimated rates of gas production also date from 2 to 4 decades ago. Herein, we summarize the recent application of modern microbiological tools as well as recent metadata analysis using California, USEPA and international data to outline an evolving view of landfill biogeochemical/microbiological processes and rates. We focus on United States landfills because these are uniformly subject to stringent national and state requirements for design, operations, monitoring, and reporting. From a microbiological perspective, because anoxic conditions and methanogenesis are rapidly established after daily burial of waste and application of cover soil, the >1000 United States landfills with thicknesses up to >100 m form a large ubiquitous group of dispersed 'dark' ecosystems dominated by anaerobic microbial decomposition pathways for food, garden waste, and paper substrates. We review past findings of landfill ecosystem processes, and reflect on the potential impact that application of modern sequencing technologies (e.g., high throughput platforms) could have on this area of research. Moreover, due to the ever evolving composition of landfilled waste reflecting transient societal practices, we also consider unusual microbial processes known or suspected to occur in landfill settings, and posit areas of research that will be needed in coming decades. With growing concerns about greenhouse gas emissions and controls, the increase of chemicals of emerging concern in the waste stream, and the potential resource that waste streams represent, application of modernized molecular and microbiological methods to landfill ecosystem research is of paramount importance.

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“…in the disruption of the ionic current. By measuring the disruption of the ionic current, the molecule is identified (Patel et al, 2018).…”

Section: A Comparison Of Hts Platforms For the Study Of The Gut Microbiomementioning

confidence: 99%

Comparison of four high throughput sequencing platforms in a medical laboratory for gut microbiome research

Das¹,

Dadwal²,

Radhakrishnan³

et al. 2020

ijah

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Next Generation Sequencing (NGS) systems, which are more appropriately called High Throughput Sequencing (HTS) systems have revolutionized the way microbiome of a given environment may be studied in considerable details. The reach of HTS is significantly more than that of the standards of Sanger sequencing, and the results from the study of gut microbiome and other metagenomic research has shown that HTS is going to remain as an indispensable tool for such studies for some time to come. Microbiology laboratories working in the field of human medicine, veterinary medicine, agriculture or environmental sciences would need to know and understand the intricacies of HTS methods. This would entail not only a theoretical understanding of the principles of HTS, but also a practical know how about processes, consumables, pitfalls and costs associated with HTS. The current review attempts to explain this important but complex topic with the help of a comparative description of various HTS/NGS systems available in a cancer hospital in eastern India, which is engaged in the use of such technologies for patient care and basic research.

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MinION rapid sequencing: Review of potential applications in neurosurgery

Cited by 22 publications

References 65 publications

Epigenetic alterations in glioblastomas: Diagnostic, prognostic and therapeutic relevance

Epigenetic alterations in glioblastomas: Diagnostic, prognostic and therapeutic relevance

A Review of Landfill Microbiology and Ecology: A Call for Modernization With ‘Next Generation’ Technology

Comparison of four high throughput sequencing platforms in a medical laboratory for gut microbiome research

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