Sequencing Technologies in Clinical Research

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    "description": "Nanopore-based sequencing has become a highly effective next generation sequencing tool for biological research. Nanopore sequencing converts the electrical signals generated by a nucleotide strand (either DNA or RNA) passing through the nanopore into the base sequence. This methodology was exclusively commercialized by Oxford Nanopore Technologies, allowing sequencing of long reads with real-time sequence detection and analysis. It can also provide base modification detection. The technique has short sample preparation times with low instrument costs. The technology is a relatively new, rapidly expanding and groundbreaking, with ~79% of nanopore-related literature published within the last 5 years (determined from PUBMED publication stats). The design of nanopore devices has given this technology greater versatility/flexibility than other sequencing platforms. Allowing work to occur out in the field (using a portable sequencing device) or within a traditional lab research setting. A portable version of Nanopore have been used in randomised clinical trial to produce real-time near-complete genome sequencing of viruses isolated from clinical samples. This study suggests a future role of this portable technique in virus infection monitoring for early detection in diverse populations. As well as analysis of human samples and long-read sequencing of bacterial genomes. Prof Beggs research group has been as the forefront of the optimisation and deployment of Nanopore sequencing technologies in clinical research. This work that has been disseminated in multiple peer-reviewed publications (in 2018, 2020, 2021 and 2023). Beggs group have used this unique technology to address existing clinical questions such as \"how we can improve HLA typing, by potentially reducing process time and cost\", aiming to generate a rapid single-tube assay? Nanopore dependent-research (within Cancer and Genomic Sciences) and service support (from Genomics Birmingham) are essential for our work and supporting the sequencing of internal and external clients, now and moving forward. Illumina and Nanopore sequencing are currently used routinely within our labs. Both rapidly sequence DNA or RNA and produced rapid and highly accurate genomic, transcriptomic and epigenomic data. Below are some of the specific, unique properties of Oxford Nanopore technologies (using either the GridIon or PromethION 24 sequencers). This summary was supplied by the manufacturer. 1. Nanopore devices (GridIon, MinION and PromethION 24) can sequence native DNA and RNA from fragment sizes of 20 bp to millions of bases for up to 5 independent MinION or Flongle Flow Cells or 24 independent PromethION Flow Cells, gaining coverage of ~30X per human genome per flow cell. 2. The allow direct, PCR-free sequencing of DNA and RNA 3. Providing standard (FASTQ and BAM) output files, the latter including epigenetic modifications for 5mC and 5hmC methylation apart from the standard bases. 4. They perform Real-time sequencing, with integrated compute enabling real-time basecalling including modifications (5mC and 5hmC, high accuracy basecalling model). 5. With real-time data analysis, e.g., aligning to reference directly from the device software. 6. Sequencing continues until a defined coverage is met and/or define a specific run time for your sequencing run. 7. Sequencing libraries can be used with any Oxford Nanopore device, allowing for instance to conduct library quality control on a lower capacity device prior to generating data on a high-capacity instrument. 8. There are rapid library preparation solutions (from 10 minutes) as well as automatable, high-throughput library preparation that can be performed on various liquid handlers from as little as 3.5 hours for 96 samples. 9. Post sequencing, the library can potentially be covered from the flow cell, and re-sequenced on another flow cell to increase output. Nanopore technology is the only supplier of these unique products, equipment and support services, we need to continue our specific work. We require this VEAT to allow us access to these niche products/ services, so we can continue to support cutting-edge research. This will potentially lead to the development of new Genomics Birmingham Nanopore services for both research and clinical projects in the near future.",
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