Join us for the inaugural Novogene European user forum. We have gathered speakers from academia and industry to create a unique event that will give you an insight into some exciting new research projects and provide an overview of where the NGS industry is headed. Add to this some expert speakers from Novogene and we have all the ingredients for an exceptional learning experience. There is no cost to attend the forum.
The User Forum will be held online and runs over two mornings 9.00 - 11.30 BST / 10.00 - 12.30 CET.
Introduction to Novogene Genomic Services & Solutions
Novogene is a world-leader in Next Generation Sequencing and Bioinformatics. From our state-of-the-art facility in Cambridge UK, our leading-edge platforms, well-developed bioinformatics pipeline, extensive NGS experience, and highly skilled and supportive team help life science research and development organizations advance human health, agriculture and environmental protection.
In this section, we will go over the diverse genomic services and solutions in Novogene, and potential support for customized collaborations.
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Harnessing genetic diversity in wheat and its wild relatives for disease resistance
Molecular cloning of genes underpinning genetic variation opens up novel precision-deployment possibilities via marker-assisted selection, gene editing and transgenesis. However, large genomes, extensive regions of suppressed recombination, and long generation times, often impose significant barriers to gene cloning in crops and their wild relatives.
Faced with these challenges, we have developed fast and efficient methods for gene discovery and cloning which use mutant and natural populations followed by sequence alignment to locate genes [1-5]. We also developed a method for halving the generation time of wheat and other crops, in a controlled environment, dramatically speeding up capabilities for research and breeding purposes [6-7].
Our focus is on wheat and major diseases of wheat, including the rusts, blast and Septoria. Our long-term aim is to use conventional genetics or transgenesis to engineer pyramids of resistance genes for more durable resistance against major diseases of wheat [8-9]. We propose an internationally coordinated effort to generate a wheat resistance gene atlas to facilitate more judicious deployment of resistance genes in GM and conventional breeding programmes.
1. Steuernagel et al (2016). NLR-parser: a tool to rapidly annotate the NLR complement from sequenced plant genomes. Bioinformatics 15;31(10):1665-7.
2. Steuernagel et al (2016). Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nature Biotechnology 34:652-5.
3. Sánchez-Martín et al (2016). Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biology 17(1):221.
4. Arora et al (2019) Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nature Biotechnology 37:139-143.
5. Steuernagel et al (2020) NLR-Annotator enables annotation of the intracellular immune receptor repertoire. Plant Physiology, DOI: https://doi.org/10.1104/pp.19.01273
6. Watson et al (2018). Speed breeding is a powerful tool to accelerate crop research and breeding. Nature Plants 4:23-29.
7. Ghosh et al (2018). Speed breeding in growth chambers and glasshouses for crop breeding and model plant research. Nature Protocols 13:2944-2963.
8. Dhugga and Wulff (2018) Wheat, the cereal abandoned by GM. Science 361:451-452.
9. Wulff and Jones (2020). Breeding a fungal gene into wheat. Science 368:822-823.
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Introduction to Novogene Genomic Services & Solutions
Novogene is a world-leader in Next Generation Sequencing and Bioinformatics. From our state-of-the-art facility in Cambridge UK, our leading-edge platforms, well-developed bioinformatics pipeline, extensive NGS experience, and highly skilled and supportive team help life science research and development organizations advance human health, agriculture and environmental protection.
In this section, we will go over the diverse genomic services and solutions in Novogene, and potential support for customized collaborations.
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Collaboratively establishing advanced bioinformatic workflows to support cancer phylogenetics
Malignant pleural Mesothelioma (MPM) is a rare, incurable cancer that is caused by exposure to asbestos. The UK has the highest incidence in the world, and its continued mining and use in developing nations, despite a worldwide ban, is set to lead to increasing global burden of this cancer in the 21st century.
The choice of effective treatments and precision therapies are lacking. MPM takes 30-50 years to form following exposure however the evolutionary pathway is unknown. understanding how mesotheliomas evolve could highlight constraints or bottlenecks that could serve as novel drug targets.
To elucidate the evolutionary histories of mesothelioma we developed a research platform, ME:DuSA (Mesothelioma Evolution: Deciphering drUggable Somatic Alterations) involving the multiregional sampling of MPMs at the time of routine surgery followed by multiregional whole exome sequencing (mWES) via Novogene. We had selected Novogene based on productive initial discussions with their global leadership in the USA in 2015.
Based on an MRC academic industry exchange grant, we set up meetings with Novogene bioinformatics and our university to explore the development of a comprehensive bioinformatics pipeline to interrogate MPM which we implemented on a pilot study involving 90 exomes in 22 patients.
The phylogenetic analysis was highly collaborative, revealed new insights into evolutionary constraints in MPM and the clinical impact of specific evolutionary trajectories (manuscript submitted).
Future studies will scale the analysis 10x to include whole genome, methylome and transcriptome integration. In parallel, we are presently conducting WES of our phase II and soon phase III trial cohorts, to examine genomic predictors of treatment efficacy. In the case of eg. PARP inhibition, we are conducting and integrate WES of primary cell lines, explants and patient tissues to support the elucidation of genomic predictors of drug sensitivity.
In summary, our collaborations have transformed our capacity to address these complex genomic questions in a collaborative environment, whilst maintaining the highest quality standards along our workflows.
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Professor Dean A. Fennell, PhD FRCP
University of Leicester and University Hospitals of Leicester NHS Trust, UK
Chair of Thoracic Medical Oncology,
Director, Leicester Mesothelioma Research Programme
Cancer Research UK Centre Experimental Medicine Centre
Dean Fennell is Professor & consultant in Thoracic Medical Oncology, and Director of the Leicester Mesothelioma Programme based at the University of Leicester and University Hospitals of Leicester in the UK. He is an internationally recognised key opinion leader, clinical investigator and translational researcher with a focus on mesothelioma. He has led several investigator-initiated trials from phase 1 through to phase III.
Prof. Fennell is member of the IASLC mesothelioma taskforce, steering committee for the British Lung Foundation mesothelioma research network, past president of the International Mesothelioma Interest Group, and co-author of the UK BTS, and European (ESMO, ERS) mesothelioma treatment guidelines. He is currently the Leicester lead for the ground breaking CRUK TraceRx/Darwin studies in lung cancer and BLF supported MEDUSA (mesothelioma) evolution studies. Prof. Fennell held two prestigious CRUK clinician scientist and MRC doctoral fellowships.
He originally trained in pharmacology (1st class) and medicine at University College London where he was awarded several prizes. He completed medical training in the London Golden circuit (Hammersmith, Brompton, Guy's, St Thomas's), and completed his specialist training at Barts Hospital. Prof. Fennell has published over 100 peer reviewed articles in journals including The Lancet, Lancet Oncology, New England Journal of Medicine, Nature, Nature Reviews Cancer, and Proceedings of the National Academy of Sciences.
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Dr Brande Wulff
John Innes Centre
Group Leader
Designing Future Wheat
Brande’s research programme explores the genetics of disease resistance in wheat.
This research has led to developing fast, new and efficient methods for gene discovery and cloning which use mutant and natural populations followed by sequence alignment to locate genes, a technique which could be applied to a range of crop plants.
Brande has also developed a method for reducing the wheat generation time to eight weeks, in a controlled environment, dramatically speeding up capabilities for research and breeding purposes.
Brande is also interested in how microbial effector proteins, their host targets, and plant immune receptors co-evolve.
His work seeks to translate knowledge of this interaction into practical solutions for genetic disease control in agricultural systems.
His focus is on bread wheat and major diseases of wheat – including stem rust, wheat blast and Septoria tritici blotch.
Brande’s long-term goal is to provide resistance gene–based solutions to prevalent disease threats of wheat in the UK and worldwide.
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Neil Ward
Senior Sales Director, North Europe
illumina Cambridge Ltd.
Neil is the Senior Director of Sales for Illumina’s Northern Europe business and has worked in the field of genomics for more than 20 years.
Neil has worked for illumina for 12 years and held various commercial roles across marketing and sales. He’s been involved in the development of many collaborations, some of which have resulted in landmark projects such as the 100,000 genomes project with Genomics England and whole genome sequencing of UK Biobank. In his previous marketing role Neil was instrumental in major product launches including platforms such as the HiSeq X and NovaSeq and more recently has been the coordinator of the co-development of the COVIDSeq assay with the Sanger institute and COG-UK consortium.
Prior to illumina, Neil studied in Manchester and has a degree in Biochemistry and an MSc in bioinformatics. After graduating he worked for four years in the biotech sector as a researcher, mining the initial human genome sequences for new drug targets. Neil then moved to commercial roles initially in a bioinformatics software company, then Agilent before joining illumina in 2008.
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The last decade has seen an amazing decline in the cost of sequencing and an resulting explosion in genomics driven applications. Today, around the world, there are multiple large genomics projects that would have been unimaginable in scale just a few years ago. We believe that genomics can play an important role in improving human health and yet we’re at the very early stages of that journey. What will a genomics powered healthcare system of the future look like and what barriers will we collectively need to break down in order to realize the promise of genomics?
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The last decade has seen an amazing decline in the cost of sequencing and an resulting explosion in genomics driven applications. Today, around the world, there are multiple large genomics projects that would have been unimaginable in scale just a few years ago. We believe that genomics can play an important role in improving human health and yet we’re at the very early stages of that journey. What will a genomics powered healthcare system of the future look like and what barriers will we collectively need to break down in order to realize the promise of genomics?
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Dr Wei Li
Senior Product Manager
Novogene Europe
Dr Wei Li got her bachelor’s degree, majoring in Life Science and Technology, from Nanjing Agriculture University, China. She then started her graduate study in Clemson University, South Carolina, USA. She completed her MS and PhD in the same lab, working on cotton plant responses to reniform nematode (a parasitic root pathogen) infection. In this project, she focused on the cotton root transcriptome and combined with physiological and pathological methods to better understand plant responses. With hundreds of candidate genes identified, I was offered a postdoc position in a plant functional genomics lab to work on a cotton transformation project. Here she used CRISPR/Cas9 systems to knockout the candidate genes and evaluate their biological functions.
Wei started at Novogene Europe in the bioinformatics department as a senior bioinformatics engineer in April 2019. in August she was promoted to senior product manager in charge of the service development for Novogene Europe in the Product department.