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Nanopore sequencing offers advantages in all areas of research. Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins.

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Catch up on the Cancer Translational Research Symposium

Tue 7th September 2021

We hope you enjoyed the Cancer Translational Research Symposium. If you would like to watch the talks from the conference again, you are in the right place! Hear from Franz-Josef Müller and Helene Kretzmer, Greg Elgar, Anna Dolnik, and Cecilia Yeung and Olga Sala Torra. 

 

Bringing nanopore sequencing to the operating room

In their presentation, Franz-Josef Müller & Helene Kretzmer discuss the possibility of intraoperative sequencing for the diagnosis of brain tumours. Towards this aim, they discuss the adoption of molecular and bioinformatic strategies necessary for realising the enormous potential of real-time nanopore analysis. Based on preliminary results, they suggest that nanopore sequencing could deliver a reliable molecular diagnosis of distinct malignant entities within the timeframe of an oncologic operation. Importantly, they identify critical areas in which health care systems-wide innovation will be required for developing intraoperative sequencing into a truly actionable diagnostic tool in the foreseeable future.

 

Cancer WGS on the PromethION

At Genomics England, in partnership with NHSE, Greg Elgar and his team are assessing the potential of long read sequencing reads for cancer whole genome sequencing (WGS) using the PromethION instrument. In a phased programme, the aim is to build a robust and resilient end-to-end pipeline for medium to high throughput WGS that provides sufficient coverage for sensitive somatic calling of structural and small variants, as well as for accurate methylation profiling. Greg's team have recently completed Phase 1, sequencing around 100 tumour:normal pairs from 3 different cancer types, where the primary objectives were to establish a set of protocols that will permit the design and scaling of a clinical pipeline, in a similar vein to the existing short read WGS pipeline for the NHS Genomic Medicine Service

 

Rapid genomic profiling of hematologic malignancies: an update

Cytogenetic analysis represents a key part of diagnostics in hematologic malignancies. In accordance, Anna Dolnik aimed to establish and validate karyotyping based on low coverage whole genome sequencing (WGS) using Oxford Nanopore technology and test its applicability in a wide spectrum of hematologic malignancies. Oxford Nanopore technology was found to provide rapid results for CNVs at high resolution of 0.1 Mbp and high reproducibility. Anna Dolnik presented an example of 50 cytogenetically aberrant well-characterised AML cases for which she compared nanopore-based profiles with conventional cytogenetic analysis.

 

Cloud computing for clinical nanopore fusion detection

Fusion genes identification is integral in management and diagnosis of leukaemia patients; however, current techniques are limited by sensitivity and range. Despite lower accuracy, fusion gene identification is suitable for nanopore sequencing as the main analytical requirement is to find reads with gene segments that do not belong together. The lack of packaged software with easy user interface for nanopore is a deterrent. Bwb is a graphical tool that allows users to link Docker container enclosed software, build, and execute workflows to be run on GPU and cloud enabled servers that accelerates analysis speed and reduces costs.

 

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