• Event
  • Science

EI Innovate: genomics data to advance bioscience

Developing solutions to global issues with EI’s advanced capabilities and expertise in genomics and bioinformatics - improving global food security, environmental management, conservation, health and wellbeing.

Event date:

13 November 2019

Time:

10h00 - 16h30

Venue:

Earlham Institute

Registration deadline:

31 October 2019

Cost:

£15

About the event.

This event will showcase our capabilities and expertise in genomics, bioinformatics, synthetic biology, crop phenotyping, and high-performance computing.

This expertise allows us to understand complex biological systems in plants and animals and their interaction with the environment, which can help to develop solutions to industrial challenges in global food security, improving human, animal and plant health, and aid conservation.

We work with a number of academic and private organisations across the agriculture, food and health sectors, as well as charities and other organisations involved in conservation and protection of biodiversity.

This event will help you to fully understand the opportunities for collaboration with EI, and how engaging with our science and services can be of benefit to you and your organisation.

Offering talks, networking and discussion groups, the event will improve awareness of the full range of our research and capabilities, and how these can be accessed.

We are also offering tours of the Earlham BIO Foundry and Genomics Pipelines facilities. Our state-of-the-art BIO Foundry provides automation to DNA assembly projects for the synthesis of molecules at the nanoscale level, while our high-throughput genomics facility hosts a number of different sequencing platforms. We embrace technology at the leading edge of innovation for development and rapid release to the bioscience community.

Target audience

We welcome individuals from organisations engaged with:

  • research utilising genomics, bioinformatics, high performance computing and statistics applied to biological systems;
  • deploying bioinformatics, data analysis, and machine learning techniques that utilise genomics data;
  • repositories of biologic materials and gene banks, botanical gardens and zoos;
  • the agri-food supply chain and biotech sector;
  • developing lab instrumentation, tools, products, and services for bioinformatics, genomics, and data analysis and integration;
  • protection of biodiversity and conservation;
  • medical diagnostic, digital healthcare, precision medicine;
  • bioprospecting;
  • investment, plus public funders and government bodies investing in research and innovation in life sciences and adjacent technologies.

Programme.

13 November 2019

**Please note that this programme is tentative and may be subject to change. More details will be added over the coming months.**

TimeTopic
09:30 - 10:00Registration opens (Coffee and networking)
10:00 - 10:10Welcome
10:10 - 10:30Decoding Living Systems - our strategy, platforms and capabilities - Professor Neil Hall, Earlham Institute
10:30 - 10:50Understanding Biodiversity through technological and algorithmic innovation - Professor Federica Di Palma, Earlham Institute
10:50 - 11:10Exploring the Genomics, Traits and Uses of Plant and Fungal Diversity - Professor Alexandre Antonelli, The Royal Botanic Gardens, Kew
11:10 - 11:40Networking break with refreshments
11:40 - 12:30

Earlham Institute: science showcase talks

1. Genomics at Single Cell Resolution - Dr Iain Macaulay

2. Data driven crop science at EI - Professor Anthony Hall

3. Portable sequencing for real-time surveillance and diagnostics - Dr Richard Leggett

4. Recoding Plant Metabolism - Dr Nicola Patron

5. Precision medicine using multi-omics and patient-derived organoids - Tamás Korcsmáros

12:30 - 13:30

Lunch and poster session / tours of EI labs

Posters:

1. Single cell technology defines cell identity and tissue heterogeneity - Dr Laura Mincarelli

2. LITE: An affordable, automated, high throughput sequencing and assembly pipeline - Dr Darren Heavens

3. ELIXIR-UK: life science data infrastructure in the UK, Europe, and beyond - Prof Neil Hall/Dr Aidan Budd

4. Understanding evolution to fight bacterial disease - Dr Matt Bawn

5. Target isoforms identification using long-read sequencing - Dr Wilfried Haerty

6. A low-cost, high-throughput method for assessing transcription factor-DNA binding affinity - Dr Nicola Patron

7. Plenty of fish: identifying tilapia species from images - Dr Felix Shaw

8. Uncovering the hidden potential of genomic variation in wheat - Dr Jon Wright

9. Tools to aid improved genome annotation - Dr David Swarbreck

10. Sustainable agriculture: predicting virulent plant pathogen emergence - Dr Mark McMullan

13:30 - 15:00

Breakout sessions

1. New Frontiers in Next-Generation Sequencing - Dr Karim Gharbi

2. Data Mining of the UK Tree of Life to Understand and Utilise Biodiversity of British Species - Dr Nicola Patron and Dr Wilfried Haerty

3. Opportunities for Genomics and Bioinformatics to Drive Biodiversity Based Bioeconomy - Professor Federica Di Palma

4. A guided discussion about the value of data for driving research, innovation and commercialisation - Dr Rob Davey

15:00 - 15:30Networking break with refreshments
15:30 - 15:50Global challenges addressed through natural history collections past, present and future - Dr Tim Littlewood. Natural History Museum, London
15:50 - 16:10

Keynote talk

Using nanopore sequencing: from first principles to applications

Dr Daniel Turner, Vice President of Applications, Oxford Nanopore Technologies Ltd

16:10 - 16:20Closing remarks from Dr Liliya Serazetdinova, Earlham Institute
16:20 - 17:00Networking and refreshments
17:00Close of event

Abstracts.

Global challenges addressed through natural history collections past, present and future

Natural history collections are often thought of as a set of curiosities and peculiarities assembled to inspire, inform, educate or perhaps just collect dust. As reference material for accurate identification (systematics and taxonomy), the majority of specimens have lived a relatively uneventful life; at least once described, catalogued and stored. In isolation, collections are limited in scope and value, with their true potential and importance understood by curators and a few researchers. Subjected to analytical, imaging and molecular interrogation specimens extend their value; enriched metadata and access provides the basis for an extended specimen.

Advances in informatics and technology offers opportunities to unlock hidden wealth in collections by providing awareness and access to the world’s billions of specimens, and tangible links between past, present and future. Collections capture diversity and change through space and time. Provenance and strategic collecting provides useful data points in space and time, but how diversity is measured, and what drives that diversity is limited only by the science applied to specimens and the informatics linking the data.

Why such items were collected and for what purpose is as diverse as the specimens themselves, with the nature and history of each specimen reflecting different scientific, social, cultural and individual proclivities of who collected what, where and when. Taking examples from museum specimens and ongoing collecting programmes in addressing issues in food security, healthcare, climate change, biodiversity assessment, conservation and other pillars underpinning UN Sustainable Development Goals to demonstrate what unlocking collections can achieve, perhaps the greatest challenge remains.

What should we collect today for tomorrow? What and how we should collect, analyse and connect towards sustainable solutions depends on innovative approaches from biotechnology, informatics, computer science and citizen science.

Exploring the Genomics, Traits and Uses of Plant and Fungal Diversity

The Royal Botanic Gardens, Kew, hosts one of the world’s most diverse collections of plant and fungal diversity, comprising over eight million accessions including seeds, living specimens and dried material.

Genomics is becoming an increasingly important part of Kew’s scientific research, providing a way to classify and characterise both collected and field material and to explore the drivers of the evolution of species and traits. Kew’s Plant and Fungal Tree of Life (PAFTOL) project is reconstructing the tree of life of all known genera and all species in selected families. We study crop species in the developing world such as yam and enset, using genomic information to put traits such as environmental resilience and nutritional and agronomic value in their evolutionary context.

We are about to begin work on the Darwin Tree of Life program, an ambitious partnership with the Sanger Institute, Earlham Institute and other UK institutions to fully sequence, assemble and annotate the genomes of all 66,000 UK species. In that project, Kew will contribute well-identified specimens from the fungal and plant kingdoms and provide expertise in data analysis. In the future, we envisage the widespread sequencing of our collected material, allowing molecular differences to be observed over the historical and geographical scope of Kew’s collecting activity.

Another major project is a collaboration with the Crop Trust, to conserve seeds from the wild relatives of 29 crop species, an essential genetic reservoir for use in future crop improvement. We also engage in specific activities in over 100 countries. A major effort in Colombia, for example, focuses on underutilised plants and fungi, through a combination of ethnobotanic surveys, value chain enhancement to enrich local livelihoods, and information dissemination via integrative websites (ColPlantA, and shortly also ColFungA).

We are exploring collaborations with Earlham to help build a strategy for Colombia to sustainably exploit, and also conserve, its unique biodiversity in the future.

Using nanopore sequencing: from first principles to applications

In this talk, we will give an overview of nanopore sequencing and our latest updates and releases, before sharing recent case studies from our Applications team.

Following an introduction to how nanopore sequencing works, we will talk through the range of sequencing devices available and in development. We will also discuss the read lengths and accuracy possible with nanopore sequencing, including recent work which is enabling higher accuracy in sequencing. Following this, we will share our progress on Pore-C, a method for generation of genome-wide, multi-contact chromatin conformation maps which can effectively resolve misassemblies and join contigs.

We will show how this method was used on a de novo assembly of the genome of cell line GM24385. Here we generated an exceptionally contiguous assembly, with an N50 of 103 Mb and a longest scaffold of 216 Mb. Furthermore, we will show how we used Pore-C to detect rearrangements and copy number changes and resolve complex structural variants in the human breast cancer cell line HCC1954.

Finally, we will present how chromatin conformation capture can be used as part of a metagenomics workflow to associate plasmids with their bacterial hosts.

Decoding Living Systems - our strategy, platforms and capabilities

EI specialises in data driven biological science by combining expertise and infrastructure in genomics, computational biology, data management, and technology development.

We work across phyla often applying tools and methods developed in model and human systems to a wide variety of species of commercial, agricultural or biomedical relevance. While the biological questions we work on are highly diverse, the approaches, using computational methods to interrogate large biological datasets, provides a focus.

An economic impact of our activity shows that EI returns over £14 to the economy for every £1 spent, however, we aim to expand our translational research through partnerships with industry and other research organisations and this Innovate event is critical to this process.

Recoding Plant Metabolism

Although unable to flee predators or sub-optimal growth conditions, plants can alter the expression-levels of thousands of genes in response to changes in their environment, extensively remodelling growth and metabolism and deploying a complex molecular armoury. These characteristics have enabled the cultivation of food crops that are grown across the planet as well as providing an astounding diversity of bioactive natural products utilised in industry and medicine.

The application of engineering principles to plant biology has enabled us to establish platforms for high-throughput, automated, experimentation at nanoscales. We are combining these approaches with genome editing technologies and comparative genomics to investigate plant metabolism and gene regulation. We are applying our knowledge to improve agricultural and nutritional traits in crops and to engineer plants as photosynthetic biomanufacturing platforms.

How real-time sequencing can help real-life problems

The Technology Algorithms Group is focused on developing computational tools to get the most out of new genomics technologies. A current focus is on utilising cheap, compact, portable nanopore sequencing for real-time diagnostics and surveillance applications. In a proof-of-concept project, we used real-time sequencing to study the microbiomes of pre-term babies at risk of the gut disease Necrotizing Enterocolitis (NEC).

Using real-time analysis facilitated by our own NanoOK RT software package, we showed that we can reliably identify potentially pathogenic taxa along with corresponding antibiotic resistance gene profiles in as little as one hour, post sequencing start. In other work, we are exploring the use of nanopore sequencing “in field” – including on-board polar research vessels in the Antarctic, where we are studying microbial communities in the oceans.

Finally, we recently published a method that utilises nanopore sequencing to understand the plant species that pollinators (e.g. bees) have been visiting. The availability of such data has important applications in ecology and agriculture.

Data driven crop science at the EI

Over the last decade crop science has become increasingly data rich, with high quality genomes now available for many of the major crops. This is match by huge amounts of genotype and phenotype data. Exploring this data is requiring new tools and approaches. It is allowing us to make new discoveries and transforming crop research and breeding. I will provide examples from across the EI of how we are using large data sets to investigate mechanisms driving genetic variation, uncovering genes and markers controlling important traits and analyse complex field images.

Genomics at Single Cell Resolution

The cell is a fundamental unit of biology – whether we are looking at complex, multi-cellular organisms (plants or animals) or bacterial cultures.

At EI, we are developing tools to analyse the genetic material of individual cells so we can explore cellular heterogeneity in microbial, plant, animal and human systems. In this talk I will give an overview of the technology platforms at EI and how we can apply them.

Precision medicine using multi-omics and patient-derived organoids

The goal of the Korcsmaros group (jointly affiliated to the Earlham Institute and the Quadram Institute) is to understand biological systems related to gut homeostasis and to facilitate precision medicine and personalised microbial therapies in the field of inflammatory bowel disease (IBD).

Intestinal homeostasis is maintained by multiple cell types, including Paneth cells and goblet cells, producing antimicrobial peptides and the mucus layer, respectively, and shaping the microbiome and regulating how our cells are interacting with it. These cell types cannot be maintained in cell culture, and their investigation has been challenging. To investigate Paneth cells and goblet cells we started working with gut organoids. Organoids are a near-physiological 3D model system accurately recapitulating in vivo phenotypes. Consequently, this in vitro model has been recognised as a major technological breakthrough tool with many biological and clinical applications, including the study of biological processes such as cell differentiation, mucus production, host-microbe interactions and cell-cell communications. Gut organoids, derived from stem cells at the base of the intestinal crypts, contain all cell type progenies normally found in the digestive tract including Paneth cells and goblet cells. We have routinely used organoids derived from mouse intestinal crypts, and generated detailed transcriptomics and proteomics data from these samples. We adapted protocols to increase the cell specific analysis potential with this system. We then combined the systems biology pipelines our group has developed with the multi-omics readout of the organoids to provide mechanistic understanding on what is happening in each intestinal cell type.

With the cutting-edge platforms of the Earlham Institute and the unique resources in the Quadram Institute, including one of Europe’s largest endoscopy centres, we are now applying these approaches on patient-derived organoids. We base our work on the multi-omics analysis of gut organoids to create computational network models of Paneth cells and goblet cells interacting with other host cells or with microbial products, and then validate the predictions in a patient-specific organoid testing system. We are planning to establish a high-throughput, organoid-based screening platform that will allow us to test microbial products and microbes (eventually microbial cocktails) on key cell types such as Paneth cells and goblet cells. Our vision is that with these innovative approaches and by combining precision medicine and systems biology, we will identify effective therapeutical options preventing the onset of IBD or relapse in a precision medicine manner.

Have any questions?

We'll be happy to support you however you need, just get in touch with our organising team.

EI Training team, training@earlham.ac.uk

Address and map.

Earlham Institute
Norwich Research Park
Norwich, Norfolk
NR4 7UZ
UK