• Event
  • Science

Genome 10K and Genome Science Conference

Start date:

Tuesday 29 August

End date:

Friday 1 September 2017

Venue:

Norwich Research Park

Organisers:

Federica Di Palma, Amanda Chong, Wilfried Haerty, Emily Angiolini, Dawn Turnbull

Registration deadline:

Early Bird Registration deadline 31 May 2017. Registration closes 31 July 2017.

Cost:

Standard Early Bird £250; Standard Late £330; Student Early Bird £150; Student Late £200; Day Delegate Early Bird £70 (per day); Day Delegate Late £100 (per day)

Genome 10K Logo
Genome Science logo

We are delighted to host both the Genome 10K 2017 conference and the Genome Science 2017 conference in parallel here in Norwich.

About the event.

For the first time, Norwich, UK will host two distinguished conferences - Genome 10K 2017; the biannual conference exploring critical topics essential for understanding how complex animal life evolved through changes in DNA and how we can use this to help save dying species; and Genome Science 2017 - an annual meeting exploring advances in genomics technology and computational methodologies as well as innovation in its application.

The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in a major tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.

The mission of the Genome 10K COS is to assemble a genomic zoo of some 10,000 vertebrate species to help to understand how complex animal life evolved through changes in DNA and use this knowledge to become better stewards of the planet.

The Genome 10K Project was founded by David Haussler, Oliver Ryder, and Stephen O'Brien, who launched the project in April 2009 at a three-day meeting at the University of California, Santa Cruz.

The Genome Science meeting started out life in 2011 as the UK Next Generation Sequencing meeting, hosted by the DeepSeq facility at the University of Nottingham. Since then it has evolved and grown to be a successful event attracting in the region of 250 delegates each year. This meeting represents a fantastic opportunity for both academia and industry to engage, sharing advances, innovations and challenges in working with -omics data.

In addition to a programme packed full of interesting sessions, we have some fantastic invited speakers who will epitomise the prestige and strength of these conferences. There will also be plenty of networking opportunities, such as the social mixer and conference dinner, as well as the poster sessions. We believe training is crucial to the success of all research projects, including the G10K project and its long-term attainment of objectives. Alongside training for early career researchers we will also include parallel Special Interest Group sessions, which will monitor progress in the sector and set new milestones of the G10K project.

Keynote speakers.

Invited speakers.

Trainers.

Talk details.

Abstract

To understand the evolution of animals, we must understand genomes and development. One of the most important discoveries in 20th century biology was the finding that widely different animal species use similar genes, such as homeobox genes, to build their embryos. But if the genes are conserved, why do animal species look so different? Does evolution subtly change the regulation of key genes, or change the number of genes, or change their protein coding sequences? Examples of all three routes have been revealed through comparative genomics, including some surprising examples of how evolution changed the number and function of homeobox genes in mammalian evolution.

About Professor Peter Holland

Peter Holland is the Linacre Professor of Zoology at the University of Oxford, UK. After a degree in Zoology from Oxford and a PhD in Genetics from London, he has held academic posts at the Universities of Reading and Oxford. His research into animal genomes and evolution, spanning marine invertebrates, fish, insects and mammals, has been recognized by award of the Kowalevsy Medal, De Snoo Medal, Linnean Medal, Frink Medal and Genetics Society Medal. He was elected to Fellowship of the Royal Society in 2003.

Abstract

Kathy’s research team have demonstrated that Tasmanian devils have extremely low levels of genetic diversity at the Major Histocompatibility Complex (MHC) providing an opportunity for Tasmanian Devil Facial Tumour Disease (DFTD), a rare contagious cancer, to spread through devil populations without encountering histocompatibility barriers. They continue this research by studying the relationship between MHC type and disease susceptibility in devil populations, as well as the impact of the emergence and evolution of DFTD strains using genomics technologies.

About Professor Kathy Belov

Professor Kathy Belov is based in the Faculty of Veterinary Science at the University of Sydney. Kathy’s research expertise covers comparative genomics and immunogenetics of Australian wildlife. As well as core research into the Tasmanian Devil Facial Tumour Disease and the genetic management of the Tasmanian devil insurance programme, Kathy’s research team have participated in the opossum, platypus and wallaby genome projects where they have gained insights into genes involved in immunity and defense.They are now working on the koala and echidna genomes. Kathy has received two Eureka awards, the Crozier medal and the Fenner medal for her research.

Abstract

Genome-wide association studies (GWAS) have long been a staple of human genetics. In the simplest case a population-matched cohort of unrelated individuals with and without a disease or trait is genotyped, and then every marker (SNP) is tested for association with the phenotype. The ease of design has allowed very large cohorts to be recruited to these studies, yielding excellent power for linking genotype to phenotype. With the recent availability of populations hundreds or thousands of sequenced bacterial isolates interest has developed in applying the same technique to relevant pathogen phenotypes such as drug resistance and invasive potential. However, the highly variable pan-genome and potentially confounding strong population structure of bacteria make GWAS difficult to apply in the same way. In this talk I will describe Sequence Element Enrichment analysis (SEER), a method we have published which overcomes these issues by using k-mers as a generalised sequence variant along with appropriate population structure corrections. SEER is freely available and scales to thousands of genomes, and has been used to discover variants affecting invasive potential of S. pyogenes and region specific patterns of B. pseudomallei. Finally, I will describe recent work which pushes the limits of GWAS, testing the contribution of rare and structural variants to bacterial phenotypes.

About John Lees

John Lees is a PhD student, primarily studying the integration of sequencing data from both host and pathogen in cases of bacterial meningitis. He is also interested in phylogenetics and methods for genotype-phenotype association in bacteria.

Abstract

How is it possible that severe early-onset disorders are mostly genetic in origin, even though the disorders are not inherited because of their effect on fitness? Genomic studies in patient-parent trios have recently indicated that most of these disorders are caused by de novo germline mutations, arising mostly in the paternal lineage.

In this presentation I will discuss our research on the causes and consequences of de novo mutations using novel genomic approaches. I will illustrate all of this using severe intellectual disability as a model, for which we are making rapid progress and now have the opportunity to provide medically relevant information to the majority of patients and families involved.

Abstract

Synthetic biology applies engineering principles to biology for the construction of novel biological systems designed for useful purposes. It advocated for standards and foundational technologies to facilitate biological engineering. Defining standards for plants has enabled us to automate parallel DNA assembly at nanoscales, removing research bottlenecks and providing the international plant community access to reusable, interoperable, characterized, standard DNA parts. We are applying these principles to programmable genome engineering tools for multiplexed targeted mutagenesis and for the development of tunable, orthologous regulatory elements, synthetic transcription factors and genetic logic gates.

About Nicola Patron

Nicola is a molecular and synthetic biologist interested in the natural and engineered transfer of genetic material between genomes of different species. Her lab is focused on engineering photosynthetic organisms for industrial biotechnology and crops that are healthier to consume and less environmentally damaging to cultivate.

Abstract

The adaptive radiations of haplochromine cichlid fish in the East African great lakes provide paradigmatic systems to study the dynamics of species formation, and of natural and sexual selection. The most extensive radiation is in Lake Malawi, where in the last million years or so one or a few ancestral populations have given rise to a flock of more than 500 species, filling almost all piscine ecological niches in the lake.

Over the past few years we have collected with collaborators over 2500 samples and sequenced the whole genomes of over 300 fish from over 100 species of Lake Malawi cichlids. All species are genetically close, with pairwise divergence typically between 0.1 and 0.25%, compared to heterozygosity between 0.05 and 0.15%. In addition to extensive incomplete lineage sorting, we see strong signals of gene flow between clades at different levels in the radiation, based on PCA, F statistics and related methods. There appear to be several long chromosomal regions exhibiting unusual phylogeny, perhaps indicative of a role for large inversions in species separation.

At a finer scale, although for close species pairs Fst can be under 20%, we also see local spikes or “islands” of high differentiation that are statistically significant under simple models of population separation, suggestive of loci under selection. Finally, at a functional level, we see higher non-synonymous to synonymous differences between species in genes involved in retinal processing, the innate immune system, oxygen transport, and a number of other pathways.

About Richard Durbin

Richard Durbin is a Senior Group Leader at the Wellcome Trust Sanger Institute, where he has been since its founding in 1992. He has been involved in a succession of large scale genome sequencing projects, including co-leading the 1000 Genomes Project. His current research is focused on studying genome variation and genome evolution, and methods for processing population scale whole genome sequencing data. He has also made many contributions to biological sequence analysis, including developing methods for sequence alignment using Hidden Markov models and suffix array methods, and developing genomic databases including Pfam, Ensembl, and TreeFam. Richard is an Honorary Professor in Computational Genomics at Cambridge University, a Member of EMBO and a Fellow of the Royal Society.

Abstract

Beth Shapiro*, Nedda Saremi, Megan Supple, Gemma Murray, Richard E. Green, Eduardo Eisirik and the puma genome sequencing consortium

Human land-use changes, including deforestation and establishment of roads and highways, can obstruct natural dispersal and migration corridors, leading to population isolation and inbreeding. Among the most affected species in North America by human land-use changes is the mountain lion, Puma concolor. Once distributed across North America, mountain lions are today found only in southern Florida and the western part of the continent.

To explore the genomic consequences of increasing isolation between mountain lion populations, we sequenced and assembled a chromosome-scale de novo genome from a mountain lion from the Santa Cruz mountains, 36M, and generate high coverage resequencing data from mountain lions from populations across North America and Brazil. Using these data, we investigated the relative timing of onset and duration of inbreeding within potentially distinct mountain lion populations. North American mountain lions contain significantly less genomic diversity than Brazilian mountain lions, but show varying levels of inbreeding that does not correspond directly to present-day barriers between them. Finally, we explore the selective consequences of inbreeding on North American mountain lions, and identify genomic changes that may have evolved as a consequence of increased interaction with humans.

About Beth Shapiro

My research aims to better understand how populations and species change through time, in particular in in response to environmental and other changes to their habitat. To address this, my group uses the latest experimental and computational approaches to analyze genetic information isolated from fossil and archived remains. I am particularly interested in learning what drives two particularly important evolutionary processes: speciation and extinction.

Abstract

The domestication of animal species was essential for the emergence of complex human societies. Despite its importance there is much about the domestication process that we still do not know. Domesticated species tend to share a suite of phenotypic traits referred to as the ‘domestication syndrome’. However, whether these phenotypic similarities are the result of convergence at the genetic level remains unclear. We generated whole-genome sequences from experimentally domesticated Norway rats and American mink, and identified genes and putatively functional variants that may underlie the phenotypic differences seen in the domesticated animals.

When we combine these data with whole-genome sequences from multiple pairs of domestic animals and their wild sister species we find biological pathways that appear to be recurrently affected by the domestication process across all domesticated animal species. One of these is the ErbB signalling pathway, involved in the development of the reproductive system and neural crest migration.

About Alex Cagan

Alex Cagan investigates evolutionary processes in somatic tissue. His research focuses on characterising mutation and selection in healthy tissues and how this relates to cancer and ageing.

Evolution is often considered to be an almost imperceptibly slow process. However, the cells that compose our own bodies are constantly acquiring mutations. Some of these mutations may influence cellular phenotypes, such as growth, resulting in clonal expansions. Over time the body may become a patchwork of clones. These processes may have profound implications for cancer progression and ageing. Due to technical limitations this evolutionary landscape has remained almost totally unexplored. I work with laser capture microdissection and genome sequencing to describe and understand processes of somatic evolution. I seek to adapt methods from comparative evolutionary genomics to gain new insights into evolution within the body.

Abstract

Associative Transcriptomics (AT) is a potent method, first developed in the crop plant Brassica napus, enabling rapid identification of gene sequence and expression markers associated with trait variation in diversity panels. It can be effective even when advanced genomic resources are unavailable, making it a valuable tool for studying traits in non-model species. Most recently, we applied AT to the problem of ash dieback disease, a fungal disease affecting ash trees which was first discovered in the UK in 2012.

Using a Danish ash diversity panel varying for susceptibility to the disease, we discovered expression-based markers that could be used to identify trees with high levels of tolerance to the disease. In addition, information about the genes in which the markers are located, is revealing clues to the mechanisms underlying the ability of some trees to tolerate the disease.

About Andrea Harper

Dr Harper's lab is focused on utilising next-generation sequencing data for the development of statistical genetic and systems biology methods, such as associative transcriptomics, to identify the underlying genetic control of important traits in plants.

Programme.

Programme Key

Open/closeG10KGenome ScienceShared SessionsTraining/EI LedBreaks

Day 1 Tuesday 29 August

08:30 - 09:00Registration
9:00

Training

Science Communications
Darwin Training Room, EI

Registration continued

12:30 - 13:00Lunch
13:00Welcome: Neil Hall and Federica Di Palma
13:30 - 14:15 Keynote 1

Towards the gapless assembly of complete vertebrate genomes
Dr Adam M. Phillipy
14:15 - 15:00 Keynote 2

Saving the Tasmanian devil from extinction
Prof Kathy Belov
15:00 - 15:30Coffee Break
15:30 - 17:45

Session 1

Vertebrate Genomics

Chair: Federica Di Palma
Invited Speaker: Alex Cagan

Session 1

Microbial Genomics

Chair: Kate Baker
Invited Speaker: John Lees

Session 1

Plant Genomics

Chair: Anthony Hall
Invited Speakers: Ksenia Krasileva/Andrea Harper

18:00Social Mixer, EI

Day 2 Wednesday 30 August

08:30 - 09:00Registration
09:00 - 10:30

Session 2

Evolutionary Genomics

Chair: Beth Shapiro
Invited Speaker: Emma Teeling

Session 2

Clinical and Translational Genomics

Chair: Jonathan Coxhead
Invited Speaker: Joris Veltmann

Session 2

Agricultural Genomics

Chair: Mick Watson
Invited Speakers: Alan Archibald/Nicola Patron

10:30 - 11:00Coffee Break
11:00 - 12:30

Session 3

Conservation Genomics

Chair: Emma Teeling
Invited Speaker: Beth Shapiro

Session 3

Developmental Biology

Chair: Aziz Aboobaker
Invited Speaker: Kristin Tessmar

Session 3

Microbial Communities

Chair: Nick Loman
Invited Speaker: TBC

12:30 - 13:30Lunch and Poster Session
13:30 - 15:00

Session 4: Sequencing Technology & Developments

Chairs: Mike Quail/Dan Swan
Invited Speaker: TBC

15:00 - 15:30Coffee Break
15:30 - 17:45

Session 5: Genome Informatics

Chair: Rob Davey
Invited Speaker: Doreen Ware

18:00Conference Dinner, The Halls, Norwich

Day 3 Thursday 31 August

08:30 - 09:00Registration
09:00 - 10:30

Session 6

Population Genomics

Chair: Wilfried Haerty
Invited Speaker: Richard Durbin

Session 6

Single Cell

Chair: Iain Macaulay
Invited Speaker: TBC

Funding Bodies/Editors

10:30 - 11:00Coffee Break
11:00 - 12:30

Funding Bodies/Editors

Sponsors Showcase

Chairs: Tim Stitt/TBC/TBC

Funding Bodies/Editors

12:30 - 13:30Lunch and Poster Session
13:30 - 14:15

Keynote 3: Homeobox genes and animal evolution: from duplication to divergence

Prof Peter Holland

14:15 - 15:00

Keynote 4: TBC

TBC

15:00Close of Conference
15:30 - 16:45Working Group 1

Training

Career Development
Darwin Training Room, EI

Day 4 Friday 1 September

08:30 - 09:00Registration
09:00 - 10:30

Working Group 2

Training: De novo assembly

25 places
Darwin Training Room, EI

Training: Introduction to Galaxy

25 places
Chris Lamb Training Suite

10:30 - 11:00Coffee Break
11:00 - 12:30

Working Group 3

12:30 - 13:30Lunch
13:30 - 15:00

Working Group 4

15:00 - 15:30Coffee Break
15:30 - 17:00

Working Group 5

Registration.

Registration is now open, you can secure your place by clicking the button below.

Registration includes:

  • Access to all lectures
  • Access to poster sessions
  • Access to a choice of special interest groups, training and CPD sessions
  • Conference Dinner
  • Optional transport to the conference venue from UEA accommodation (15 minutes’ walk)

Please note: Accommodation is not included in the registration fee. Accommodation at Paston House, UEA is optional at registration and will be added to the registration fee if selected.

Registration opens: 1 February 2017

Early Bird registration closes: 31 May 2017

Abstract submission deadline: 31 May 2017

Late registration closes: 31 July 2017

Registration details:

Early Bird Registration (1 Feb 2017 - 31 May 2017)Late Registration (1 May 2017 - 31 Jul 2017)
Standard Registration£250£330
Student Registration£150£200
Day Delegate (per day)£70£100

Abstracts.

Deadline for submission of abstracts is 31 May 2017.

Abstract submission:

1 February - 31 May 2017

You may submit an abstract during early bird registration only. You will be permitted to submit your abstract for consideration for:

  • Oral presentation
  • Poster presentation
  • Oral and poster presentation

During submission, you will be required to identify the most appropriate theme aligned to the session topics. The chair persons for that session will form the reviewers panel for your abstract.

Why submit?

  • Peer review of your work
  • A track record of your successes for your CV
  • Opens opportunities for networking
  • Can support manuscript preparation

Eligible abstracts will be subject to selection to receive travel bursaries to allow individuals to attend the conference (details to follow).

Venue.

Hosted at the Earlham Institute (EI), a cutting edge, contemporary research institute and registered charity, working in an area of rapid technological development and innovation. Established in 2009, EI is strategically funded by the BBSRC to lead the development of a skill base in bioinformatics and a genomics technology platform for UK bioscience.

The Institute is located on the Norwich Research Park, together with its partners: the John Innes Centre, the Institute of Food Research, The Sainsbury Laboratory, the University of East Anglia and the Norfolk and Norwich University Hospital. The Research Park has an excellent reputation for research in plant and microbial sciences, interdisciplinary environmental science and food, diet and health, to which EI contribute strengths in genomics and bioinformatics.

Close links exist between the NRP partners and new opportunities for collaboration in exciting new initiatives are under development. The NRP recently received £26M of government investment to facilitate innovation and further develop infrastructure to attract science and technology companies to the Park to enhance the vibrant environment and realise economic impact from research investment.

The JIC Conference Centre.

The JIC Conference Centre

Earlham Institute at night

Earlham Institute at night

Logistics.

Accommodation is reserved at Paston House, University of East Anglia (UEA), a short 15-20 minute walk from the conference venue. The cost of this is £34.00 per night, including breakfast. This is en-suite student accommodation on the UEA campus with access to shops as well as buses to Norwich city centre.

Earlham Institute has also negotiated rates at the following hotels and facilities. When booking a room, please mention that you are attending the ‘Genome 10K Conference’ to ensure that you receive our negotiated rates:

Park Farm Hotel, Hethersett is 4 miles from Earlham Institute to the south of Norwich. This hotel has leisure facilities including a pool and the preferential rate is £90 per night bed and breakfast. A taxi would be required and costs approx. £12, but could be shared at this price.

Maid’s Head Hotel, Norwich is 4.6 miles from Earlham Institute in the centre of Norwich, next to the Cathedral. Here we also attract a beneficial rate of £90 per night bed and breakfast. A taxi, if pre-ordered, would cost around £10.

Transport is arranged to take you from the conference to the conference dinner venue on Wednesday evening at 18:00 for pre-dinner reception at 19:00

Limited transport operating on a first-come, first-served basis is available from the accommodation at UEA to the conference venue.

Conference Dinner:

https://www.thehallsnorwich.com

The conference dinner will be held on 30 August 2017 at 19.30pm in St. Andrew's Hall which is the centrepiece of The Halls and is the name by which many people refer to the whole complex of buildings.

It has a fine, high-beamed ceiling, beautiful stained glass windows, limestone columns and a large polished maple floor. It was originally the nave of the friary and was completed in 1449. The size and beauty of its proportions are impressive without elaborate decoration in keeping with the friars' rule of simplicity.

The stained glass, stone carving and deeply-coloured portraits add richness to the simple backdrop of the building, adding a contemporary feel to this incredibly historical building of civic tradition - the best of both worlds.

Coaches will take you from the conference venue at 18:00 to St Andrews Hall for the conference dinner which is in the very heart of the City of Norwich.

The Norwich Arcade, in the heart of the city centre.

Norwich Arcade

About Norwich.

Norwich as a city has a lot to offer with high street shops, two shopping centres, restaurants, bars, pubs, cinemas, a bowling alley, theatres and much more. The city is also known for Norwich Cathedral (Church of England) and the Cathedral of St John the Baptist (Catholic Church) as well as Norwich Castle which is now an art gallery and museum.

You can find more information about Norwich here.

Just a short journey out of the City and you can also enjoy the Norfolk coast which spans 93 miles with a variety of beaches and coastal landscapes.

You can find more information about what Norfolk has to offer here.

Platinum.

Gold.

Silver.

Conference dinner.

Evening reception.

De novo Assembly Training Workshop.

Other supporters.

The venue.

Hosted by Earlham Institute on the Norwich Research Park, UK, enjoy world-class facilities at both EI and the John Innes Conference Centre. We also welcome you to Norwich, a city steeped in history and culture set in the middle of East Anglia.

Address and map.

John Innes Conference Centre
Norwich Research Park
Norwich
NR4 7UH
UK

Have any questions?

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

EI Genome10K Team, training@earlham.ac.uk

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