New technologies for DNA analysis – a review of the READNA Project

McGinn, Steven; Bauer, David L.V.; Brefort, Thomas; Liang, Dong; El‐Sagheer, Afaf H.; ElSharawy, Abdou; Evans, Geraint; Falk-Sörqvist, Elin; Förster, Michael; Simon, Fabrice; Freeman, Peter; Freitag, Camilla; Fritzsche, Joachim; Gibson, Spencer J.; Gullberg, Mats; Gut, Marta; Heath, Simon; Heath-Brun, Isabelle; Heron, Andrew J.; Hohlbein, Johannes; Ke, Rongqin; Lancaster, Owen; Reste, Ludovic Le; Maglia, Giovanni; Marie, Rodolphe; Mauger, Florence; Mignardi, Marco; Moens, Lotte; Oostmeijer, Jelle; Out, Ruud; Pedersen, Jonas Nyvold; Persson, Fredrik; Picaud, Vincent; Rotem, Dvir; Schracke, Nadine; Sengenès, Jennifer; Stähler, Peer F.; Stade, Björn; Stoddart, David; Teng, Xiaoyan; Veal, Colin; Zahra, Nathalie; Bayley, Hagan; Beier, Markus; Brown, Tom; Dekker, Cees; Ekström, Björn; Flyvbjerg, Henrik; Franke, André; Guenther, Simone M; Kapanidis, Achillefs N.; Kaye, Jane; Lehrach, Hans; Mangion, Jonathan; Sauer, Sascha; Schyns, E.; Tost, Jörg; Helvoort, Joop M.L.M. van; Zaag, P. J. van der; Tegenfeldt, Jonas O.; Brookes, Anthony J.; Mir, Kalim U.; Nilsson, Mats; Willcocks, James P.; Gut, Marta

doi:10.1016/j.nbt.2015.10.003

Cited by 10 publications

(6 citation statements)

References 228 publications

(162 reference statements)

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“…A rarely used technique for analyzing RNA viruses involves padlock probes (PLPs), which were initially designed to detect DNA sequences and later developed for labeling RNA sequences in cells and tissue (Andersson et al, 2012;Gyarmati et al, 2008;Ke et al, 2013;Larsson et al, 2010;Lizardi et al, 1998;Nilsson et al, 1994). PLPs function in a variety of biological samples, have high specificity and a short nucleotide recognition requirement, and can generate a localized amplified signal alone or in multiplex reactions (Bané r et al, 1998;Hardenbol et al, 2003;McGinn et al, 2016;Nilsson et al, 1997;Zieba et al, 2012). In this study, we used the versatility of PLPs to develop an in situ RNA labeling method for analyzing IAV infections.…”

Section: Introductionmentioning

confidence: 99%

Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method

et al. 2017

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Genome delivery to the proper cellular compartment for transcription and replication is a primary goal of viruses. However, methods for analyzing viral genome localization and differentiating genomes with high identity are lacking, making it difficult to investigate entry-related processes and co-examine heterogeneous RNA viral populations. Here, we present an RNA labeling approach for single-cell analysis of RNA viral replication and co-infection dynamics in situ, which uses the versatility of padlock probes. We applied this method to identify influenza A virus (IAV) infections in cells and lung tissue with single-nucleotide specificity and to classify entry and replication stages by gene segment localization. Extending the classification strategy to co-infections of IAVs with single-nucleotide variations, we found that the dependence on intracellular trafficking places a time restriction on secondary co-infections necessary for genome reassortment. Altogether, these data demonstrate how RNA viral genome labeling can help dissect entry and co-infections.

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Section: Introductionmentioning

confidence: 99%

Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method

et al. 2017

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“…The newest sequencing technologies are based upon electrochemical reading of bases of DNA as they pass through microscopic pores, and have extended the read length to 2,000 or more base pairs (50). Though long-read sequencing is currently highly prone to errors, the combination of short and long read sequencing allows the assembly of an individual genome at a relatively rapid time and low cost (51).…”

Section: Current Limitations and Future Methodsmentioning

confidence: 99%

A primer to clinical genome sequencing

Priest

2017

Current Opinion in Pediatrics

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Purpose of review Genome sequencing is now available as a clinical diagnostic test. There is a significant knowledge and translation gap for non-genetic specialists of the processes necessary to generate and interpret clinical genome sequencing. The purpose of this review is to provide a primer on contemporary clinical genome sequencing for non-genetic specialists describing the human genome project, current techniques and applications in genome sequencing, limitations of current technology, and techniques on the horizon. Recent Findings As currently implemented, genome sequencing compares short pieces of an individual’s genome to a reference sequence developed by the human genome project. Genome sequencing may be used for obtaining timely diagnostic information, cancer pharmacogenomics, or in clinical cases when previous genetic testing has not revealed a clear diagnosis. At present, the implementation of clinical genome sequencing is limited by the availability of clinicians qualified for interpretation, and current techniques in used clinical testing do not detect all types of genetic variation present in a single genome. Summary Clinicians considering a genetic diagnosis have wide array of testing choices which now includes genome sequencing. Though not a comprehensive test in its current form, genome sequencing offers more information than gene-panel or exome sequencing and has the potential to replace targeted single-gene or gene-panel testing in many clinical scenarios.

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“…DNA analysis plays a huge role in diagnosing infectious diseases, identifying people in forensic and paternity testing, typing tissues for histocompatibility. In addition, only DNA detection methods allow obtaining unambiguous results in large-scale genetic studies that identify alleles of hereditary diseases [ 90 , 91 ]. The genotyping method is widely used in various formats of highly sensitive and specific analysis [ 92 ].…”

Section: Fpa Of Nucleic Acidsmentioning

confidence: 99%

Fluorescence Polarization-Based Bioassays: New Horizons

Hendrickson

Taranova

Zherdev

et al. 2020

Sensors

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Fluorescence polarization holds considerable promise for bioanalytical systems because it allows the detection of selective interactions in real time and a choice of fluorophores, the detection of which the biosample matrix does not influence; thus, their choice simplifies and accelerates the preparation of samples. For decades, these possibilities were successfully applied in fluorescence polarization immunoassays based on differences in the polarization of fluorophore emissions excited by plane-polarized light, whether in a free state or as part of an immune complex. However, the results of recent studies demonstrate the efficacy of fluorescence polarization as a detected signal in many bioanalytical methods. This review summarizes and comparatively characterizes these developments. It considers the integration of fluorescence polarization with the use of alternative receptor molecules and various fluorophores; different schemes for the formation of detectable complexes and the amplification of the signals generated by them. New techniques for the detection of metal ions, nucleic acids, and enzymatic reactions based on fluorescence polarization are also considered.

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New technologies for DNA analysis – a review of the READNA Project

Cited by 10 publications

References 228 publications

Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method

Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method

A primer to clinical genome sequencing

Fluorescence Polarization-Based Bioassays: New Horizons

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