WYMM Tour: Oxford
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20 February 2024, 10:00 - 17:40 GMT - Oxford, United Kingdom
Generate ultra-rich data for answers with impact.
Who says you can’t see it all? With a comprehensive view of structural variants and methylation, nanopore technology powers the bigger and bolder research questions you’ve always wanted to ask.
Join us on Tuesday 20th February 2024 in Oxford to hear from local experts who are breaking new ground in human genomics, using nanopore technology.
What you're missing matters. Stay on top of what's next.
Aside from talks ranging from human genomics for rare disease, to sequencing for cancer research, the full-day agenda will include networking breaks, Q&A, product displays, and opportunities to engage with your peers and nanopore experts.
Please note that this is an in-person event.
There is no delegate fee for this event, but registration is required. Lunch and refreshments will be provided. Your place at this event will be confirmed via email from events@nanoporetech.com.
Agenda
10:00 – 20:00 hrs GMT | Agenda (subject to change) | |
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10:00 – 11:00 hrs | Registration, breakfast and networking | |
11:00 – 11:25 hrs | What you're missing matters: Catching the unnoticed | Tonya McSherry, Oxford Nanopore Technologies |
11:25 – 12:00 hrs | Translating Oxford Nanopore Technology whole genome sequencing into clinical practice | Richard Scott and Emma McCargow, Genomics England |
12:00 – 12:30 hrs | Brain tumour classification with nanopore sequencing | Simon Paine, Nottingham University Hospitals NHS Trust |
12:30 – 14:15 hrs | Lunch | |
14:15 – 14:40 hrs | Oxford Nanopore Technologies bioinformatics update | Philipp Rescheneder, Oxford Nanopore Technologies |
14:40 – 15:05 hrs | Integrating short and long read RNA sequencing to study the human heart at single cell resolution | James Cranley, Teichmann Group, Sanger Institute |
15:05– 15:30 hrs | Present opportunities and challenges for genome-based diagnostics | Tim Aitman, University of Edinburgh |
15:30– 16:30 hrs | Networking session | |
16:30 – 17:00 hrs | Panel discussion: The future of nanopore sequencing in clinical research | Moderated by Chris Swagell, Oxford Nanopore Technologies |
17:00 – 17:30 hrs | Evaluating the diagnostic potential of long reads for rare genetic diseases | Stephan Ossowski, University of Tübingen |
17:30 – 17:40 hrs | Closing remarks | Oxford Nanopore Technologies |
17:40 – 20:00 hrs | Drinks reception |
Speakers
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Richard Scott, CEO, Genomics EnglandDr Richard Scott joined the organisation in 2015. He is also a Consultant and Honorary Senior Lecturer in Clinical Genetics at Great Ormond Street Hospital for Children and the UCL Institute of Child Health where his practice focuses on diagnosing children with rare multisystem disorders.
Richard trained in medicine at Cambridge University and University College London. He specialised in Paediatrics and subsequently Clinical Genetics in London and completed his PhD on childhood cancer syndromes at the Institute of Cancer Research.
Through his clinical practice and in his role at Genomics England he is passionate about harnessing the power of new genomic technologies for the benefit of patients in mainstream healthcare.
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Emma McCargow, Programme Lead, Cancer 2.0, Genomics EnglandClassifying tumours of the central nervous system (CNS) is challenging and typically requires comprehensive molecular analyses. In this context, the ability of Oxford Nanopore Technology to perform methylation analysis and copy-number profiling along with parallel single-gene methylation, structural variant and mutational analyses is very attractive. The small footprint and rapidity of this technology are such that analyses could be undertaken close to the patient, with the potential for key molecular findings to be delivered within an intra-operative time-frame. Together, these features bring the prospect of a paradigm shift in the way that CNS tumours are classified.
Classifying tumours of the central nervous system (CNS) is challenging and typically requires comprehensive molecular analyses. In this context, the ability of Oxford Nanopore Technology to perform methylation analysis and copy-number profiling along with parallel single-gene methylation, structural variant and mutational analyses is very attractive. The small footprint and rapidity of this technology are such that analyses could be undertaken close to the patient, with the potential for key molecular findings to be delivered within an intra-operative time-frame. Together, these features bring the prospect of a paradigm shift in the way that CNS tumours are classified.
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Simon Paine, University of NottinghamExome and genome sequencing using short read technology, has become commoditised and, although still standard, is losing its prescience in the research and clinical arenas. Single molecule, long read sequencing is gaining ground both in terms of cost and applicability. As well as providing longer reads which provide better genome coverage and capability for structural variant detection, direct reading of epigenetic modifications gives additional data without additional laboratory protocols or nucleic acid manipulation. Here, we utilise Oxford Nanopore sequencing for structural variant detection in difficult-to-diagnose cases of rare disease and are investigating the potential of direct analysis of DNA methylation by single molecule sequencing for liquid biopsy.
Exome and genome sequencing using short read technology, has become commoditised and, although still standard, is losing its prescience in the research and clinical arenas. Single molecule, long read sequencing is gaining ground both in terms of cost and applicability. As well as providing longer reads which provide better genome coverage and capability for structural variant detection, direct reading of epigenetic modifications gives additional data without additional laboratory protocols or nucleic acid manipulation. Here, we utilise Oxford Nanopore sequencing for structural variant detection in difficult-to-diagnose cases of rare disease and are investigating the potential of direct analysis of DNA methylation by single molecule sequencing for liquid biopsy.
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Tim Aitman, University of Edinburgh)
James Cranley, Sanger InstituteReconstruction of complex genomic regions containing recent segmental duplications, repeat expansions or complex structural variants has been challenging using short read sequencing methods. These regions, however, potentially harbor a substantial fraction of disease-causing variants missed in unsolved rare disease cases (still around 50% of all cases). The introduction of Nanopore long-read genome sequencing (LR-GS) into clinical genetic testing promises to reduce this gap by resolving complex genomic regions, facilitating haplotype-phasing and revealing complex SVs that often consist of closely located inversions, tandem-duplications and deletions.
Therefore, a study group consisting of four German university hospitals was launched aiming to evaluate the added diagnostic value of Nanopore LR-GS and to demonstrate its sustainability in clinical practice. The study group relies on established collaborative structures with multidisciplinary teams, data analysis task forces (DATFs), and data interpretation task forces (DITFs). We analyzed a cohort of solved cases featuring causal repeat expansions, variants in duplicate genes, complex rearrangements, and aberrant DNA methylation. We included multiple GiaB samples to benchmark variant detection methods for accreditation of LR-GS. The experience gain from the initial pilot serves as a blueprint for the analysis of a larger clinical cohort (>1000 samples).
In this talk I will focus on our experience with the bioinformatics analysis of Nanopore LR-GS data for rare disease diagnostics, including development and/or application of tools and pipelines for SNV, indel and SV detection, haplotype phasing, length estimation for repeat expansions, genotyping in duplicate genes and haplotype-specific DNA methylation analysis. I will discuss our quality criteria and benchmarking efforts and demonstrate the need for generating large Nanopore LR-GS background dataset to facilitate systemic filtering and efficient clinical interpretation of SVs in clinical diagnostics.
Reconstruction of complex genomic regions containing recent segmental duplications, repeat expansions or complex structural variants has been challenging using short read sequencing methods. These regions, however, potentially harbor a substantial fraction of disease-causing variants missed in unsolved rare disease cases (still around 50% of all cases). The introduction of Nanopore long-read genome sequencing (LR-GS) into clinical genetic testing promises to reduce this gap by resolving complex genomic regions, facilitating haplotype-phasing and revealing complex SVs that often consist of closely located inversions, tandem-duplications and deletions.
Therefore, a study group consisting of four German university hospitals was launched aiming to evaluate the added diagnostic value of Nanopore LR-GS and to demonstrate its sustainability in clinical practice. The study group relies on established collaborative structures with multidisciplinary teams, data analysis task forces (DATFs), and data interpretation task forces (DITFs). We analyzed a cohort of solved cases featuring causal repeat expansions, variants in duplicate genes, complex rearrangements, and aberrant DNA methylation. We included multiple GiaB samples to benchmark variant detection methods for accreditation of LR-GS. The experience gain from the initial pilot serves as a blueprint for the analysis of a larger clinical cohort (>1000 samples).
In this talk I will focus on our experience with the bioinformatics analysis of Nanopore LR-GS data for rare disease diagnostics, including development and/or application of tools and pipelines for SNV, indel and SV detection, haplotype phasing, length estimation for repeat expansions, genotyping in duplicate genes and haplotype-specific DNA methylation analysis. I will discuss our quality criteria and benchmarking efforts and demonstrate the need for generating large Nanopore LR-GS background dataset to facilitate systemic filtering and efficient clinical interpretation of SVs in clinical diagnostics.
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Stephan Ossowski, University of Tübingen
