Accelerated discovery of functional non-coding genomic variation using single molecule real-time (SMRT) sequencing.

Lead Research Organisation: University of Exeter
Department Name: University of Exeter Medical School

Abstract

The last decade has seen tremendous advances in our understanding about the role of genetic variation in health and disease, driven largely by developments in technology for sequencing the genome. Genes involved in a spectrum of debilitating disorders and health-related traits have been identified, including many by researchers at the University of Exeter Medical School, and these discoveries are starting to directly impact upon clinical practice. Despite this success, however, many regions of the genome remain hidden to contemporary first- and second-generation sequencing approaches. These include highly complex stretches of repetitive DNA and regions harbouring other types of genetic variation such as deletions and duplications. Furthermore, because the sequencing reads generated by current approaches are relatively short, they cannot be used to examine the long-distance relationships between more distal variants, nor explore the extent to which different genes are expressed in different versions in health and disease. Finally, most focus in disease genetics has been on regions of the genome that actually encode specific genes, ignoring the role of regulatory variation occurring outside of these regions. Of note, current sequencing approaches cannot be used to directly detect the presence of non-sequence-based epigenetic modifications and explore their role in disease. In this application we are requesting funds to support the acquisition of "third generation" sequencing technology, which will enable us to fully characterise genomic complexity. We are also requesting funds to support the high-performance computing infrastructure needed to store and analyse this complex data. Our aim is to advance genomics research into diabetes, neurological and other medical conditions by defining functional genetic and epigenetic variation in non-coding regions of the human genome.

Technical Summary

We are requesting funds to develop our genomic sequencing infrastructure, primarily through the acquisition of a Pacific Biosciences single molecule real-time (SMRT) sequencing system, making us one of only a handful of institutes in Europe to have such capability. This system will enable us to assay, identify and analyse regions of the genome hidden from current methods for gene discovery, and facilitate research into the functional mechanisms involved in disease. The Pacific Biosciences RS II SMRT Sequencing System provides the highest consensus accuracy and longest read lengths of any sequencing technology; current average read-lengths are >8.5kb (with a maximum of ~50kb). SMRT sequencing will facilitate advances in disease characterisation, stratification and diagnosis via its unique utility for de novo assembly across highly complex regions of the genome, targeted re-sequencing, long-range phasing of genetic variation, and epigenomic analysis via the direct allele-specific detection of modified DNA bases. We will also develop our High-Performance Computing/Informatics Infrastructure to enable the storage, analysis, alignment, and assembly of SMRT sequencing data. This infrastructure investment will enable the world-leading genetic and epigenetic research groups at the University of Exeter Medical School to further develop their innovative program of clinical genomic research in human disease, with a specific focus on diabetes and neurological phenotypes.

Planned Impact

In addition to other scientists (especially other and research groups investigating the role of genetics in diabetes and neurological diseases) the data generated using the new sequencing infrastructure has the potential to impact on a number of other beneficiaries. These include patients, the pharmaceutical industry, health service providers, and academic groups investigating the causes of other disease phenotypes and functional genomics. Existing genetics research by Exeter groups has already made significant impact in terms of understanding the causes of disease and the mechanisms behind disease progression (see description in the Case for Support), with tangible patient benefit. For example, Professor Hattersley's group discovered that patients with neonatal diabetes caused by K-ATP channel mutations demonstrate a remarkable improvement in glycaemic control when sulphonylurea tablets replace insulin injections. Quality of life has also been improved for many patients with maturity onset diabetes of the young (MODY) who have either stopped treatment or transferred from insulin to sulphonylureas as a consequence of their genetic diagnosis. The ability of SMRT sequencing to interrogate regions of the genome hidden from second generation sequencing, in addition to epigenetic and transcriptomic variation, will identify additional pathways to disease that we hope to have similar impact on clinical diagnosis, prognosis, and treatment.

Publications

10 25 50
 
Description ARUK Project Grant
Amount £433,549 (GBP)
Funding ID ARUK-PG2018B-016 
Organisation Alzheimer's Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2019 
End 02/2022
 
Description CASE STUDENTSHIP
Amount £100,000 (GBP)
Funding ID MR/P016227/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 09/2017 
End 09/2021
 
Description Establishment of a single cell isolation platform for identification of heavy and light1 chains in the antibody repertoire using PacBio sequencing" MRC Proximity to Discovery Grant, University of Exeter (S.Pagliara & K.Paszkiewicz, £137,427
Amount £137,427 (GBP)
Organisation University of Exeter 
Sector Academic/University
Country United Kingdom
Start 03/2016 
End 12/2016
 
Description NARSAD YOUNG INVESTIGATOR [EILIS HANNON]
Amount $70,000 (USD)
Organisation Brain & Behaviour Research Foundation 
Sector Charity/Non Profit
Country United States
Start 01/2018 
End 12/2019
 
Description Research grant
Amount £1,012,743 (GBP)
Funding ID MR/R005176/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 01/2018 
End 12/2020
 
Description SFARI Research Grant
Amount $975,000 (USD)
Organisation Simons Foundation 
Sector Charity/Non Profit
Country United States
Start 02/2018 
End 02/2021
 
Description University of Exeter - SMRT Pump-priming funds
Amount £50,000 (GBP)
Organisation University of Exeter 
Sector Academic/University
Country United Kingdom
Start 01/2016 
End 07/2016
 
Description Collaboration with Eli Lilly & Co 
Organisation Eli Lilly & Company Ltd
Country United Kingdom 
Sector Private 
PI Contribution We have begun working extensively with collaborators at Eli Lilly on projects spanning neuroscience, genomics, dementia and schizophrenia. We now have a joint grant funded and two CASE PhD students.
Collaborator Contribution Access to transgenic models and resources for research studies Access to laboratory facilities and compounds Co-funding of students
Impact We have submitted several grant applications, and have been funded by ARUK to undertake a joint project on rodent models of neuropathology. We have successfully applied for funding for two CASE PhD students [one MRC, one BBSRC]
Start Year 2016
 
Description Collaboration with The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPsych) and Minerva consortia 
Organisation Aarhus University
Country Denmark 
Sector Academic/University 
PI Contribution We are working extensively on DNA methylation analyses of dried blood spots collected at birth to identify molecular biomarkers of prenatal exposures and risk for developing psychiatric illness.
Collaborator Contribution We have played an integral role in analysing and generating DNAS methylation data from Danish blood spot data. I am a member of the Scientific Advisory Board for iPsych.
Impact We have been involved in several collaborative research projects, with several papers already published and other in preparation.
Start Year 2016
 
Description Collaboration with The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPsych) and Minerva consortia 
Organisation Icahn School of Medicine at Mount Sinai
Country United States 
Sector Academic/University 
PI Contribution We are working extensively on DNA methylation analyses of dried blood spots collected at birth to identify molecular biomarkers of prenatal exposures and risk for developing psychiatric illness.
Collaborator Contribution We have played an integral role in analysing and generating DNAS methylation data from Danish blood spot data. I am a member of the Scientific Advisory Board for iPsych.
Impact We have been involved in several collaborative research projects, with several papers already published and other in preparation.
Start Year 2016
 
Description 2017 WORKSHOP ON GENOMICS, CESKY KRUMLOV 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The Workshop on Genomics was developed in response to the increasing demand for training on how to effectively analyze and manage data generated by modern sequencing technologies. The Workshop curriculum includes extensive coverage of fundamental techniques required of all studies utilizing modern sequence data. This includes management and modification of modern sequence data files, using the Unix command-line and editors to manipulate large data files, assembly and best practices for sequence data generation, management and analysis. The second-half of the Workshop is devoted to specific sub-disciplines within the genomic sciences. While these topics may change from year-to-year, efforts are made to devote significant amounts of time to techniques being used widely in the field (e.g. transcriptomics, genome assembly, metagenomics, population genomics).
Year(s) Of Engagement Activity 2017
URL http://evomics.org/workshops/workshop-on-genomics/2017-workshop-on-genomics-cesky-krumlov/
 
Description 2018 Paul Janssen Lecture at IoPPN 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The Paul Janssen Lecture has been a regular feature of the academic calendar at the Institute of Psychiatry, Psychology & Neuroscience for nearly 20 years.
Lecturers are chosen on the basis of their global eminence in the field of neuroscience with a focus on schizophrenia. The annual lecture is named in honour of Belgian pharmacologist Paul Janssen (1926-2003) noted for discovering various drugs important to psychiatry, such as haloperidol, and who founded Janssen - the pharmaceutical company which sponsors the event.
Year(s) Of Engagement Activity 2018
URL https://www.kcl.ac.uk/ioppn/news/special-events/paul-janssen-lecture
 
Description Brain Awareness Week Public Lecture 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact As part of the inaugural Exeter Brain Awareness Week, I gave a public (lay) presentation on our research into genomics of schizophrenia.
Year(s) Of Engagement Activity 2018
URL http://www.exeter.ac.uk/news/events/details/index.php?event=8040
 
Description British Society for Research on Aging Meeing - Keynote Lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Professor Mill presented latest findings from brain genomics studies in context of ageing.
Year(s) Of Engagement Activity 2017
URL http://bsra.org.uk/bsra-2017-university-exeter/
 
Description Epigenomics of Common Diseases Meeting - Wellcome Trust 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Our group presented a series of posters and talks on data generated by our MRC funding.
Year(s) Of Engagement Activity 2017
URL https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=638
 
Description Feature article on our research in British Neuroscience Association (BNA) Newsletter 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The BNA interviewed me, and wrote a feature article on our work.
Year(s) Of Engagement Activity 2016
URL https://www.bna.org.uk/publications/bna-bulletin/
 
Description International Molecular Pathology Symposium - Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Professor Mill gave an invited talk at the 2017 International Molecular Pathology Symposium. He discussed current advances in using genomics in molecular pathology. There was considerable discussion following the even and several new collaborations established.
Year(s) Of Engagement Activity 2017
URL https://www.ed.ac.uk/centre-genomic-medicine/news-events/news-2017/international-molecular-pathology...
 
Description Invited Lecture - Radboud University, Nijmegen 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact Professor Mill was invited to give a lecture at Radboud University in Nijmegen, The Netherlands; hosted by Barbara Franke. He presented an overview of our work on epigenetic analyses of mental health including schizophrenia. He also gave an overview of novel genomic sequencing technologies. The lecture sparked considerable discussion and several new potential collaborations.
Year(s) Of Engagement Activity 2017
URL http://www.ru.nl/english/people/franke-b/
 
Description Invited speaker at the "Epigenetics in the Nervous System" meeting in Stockholm 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave an invited presentation at this international meeting sponsored by Abcam. There was considerable discussion and interest in our work, and several new collaborative opportunities arising from this are being explored.
Year(s) Of Engagement Activity 2018
URL http://docs.abcam.com/pdf/events/stockholm-2018-program.pdf
 
Description Invited speaker at the 2018 International Human Epigenome Consortium (IHEC) meeting in Hong Kong 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was an invited speaker at the 2018 IHEC meeting which brings together researchers from around the world working on epigenomics. I presented our ongoing work to leaders in the field and established new collaborations with other international groups.
Year(s) Of Engagement Activity 2018
URL http://ihec-epigenomes.org/news-events/hong-kong-2018/
 
Description Invited talk - Genome Institute of Singapore 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Professor Mill gave a presentation and established new collaborations at GIS and other institutions in Singapore.
Year(s) Of Engagement Activity 2017
URL http://www.gis.a-star.edu.sg
 
Description Long-reads, single-cells and cream teas -- Third-generation sequencing meeting / workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We organised a day workshop and conference to launch our MRC Clinical Infrastructure project. It was a great success with atendees from across the UK and international speakers. Programme below:
1st September 2015, University of Exeter, U.K.

Location: RILD Building, RD&E Hospital (directions here).

To celebrate the launch of our MRC Clinical Infrastructure and our new Pacific Biosciences instrument, we'd like to invite you to a special one-day meeting.

09:00 - 09:45 Tea/coffee

09:45 - 10:00 Welcome

10:00 - 10:30 Introduction to PacBio, Steve Picton Pacific Biosciences

10:30 - 11:00 Introduction to Oxford Nanopore, James Brayer/Oliver Hartwell Oxford Nanopore Technologies

11:15 - 12:00 18 months of PacBio sequencing - John Kenny, Liverpool Centre for Genomic Research

12:00 - 13:00 Lunch

13:00 - 14:00 Single cell genomics at Joint Genome Institute, Tanja Woyke

14:00 -14:45 Evolutionary genomics with PacBio - Alistair Darby, University of Liverpool

14:45 - 15:30 Clinical and bacterial applications of long-read sequencing - Nick Loman, University of Birmingham

15:30 - 16:15 Tea/coffee

16:15 - 17:15 Genomics at the New York Genome Centre, Mike Zody

17:15 - 18:15 Genome Sciences at University Washington, School of Medicine, Evan Eichler

Followed by an evening meal at the Cosy Club, Exeter.
Year(s) Of Engagement Activity 2015
URL http://sequencing.exeter.ac.uk/long_reads_and_cream_teas/
 
Description MRC Expert Group Meeting on Human Brain Research 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact We discussed optimal approaches for using human brain tissue in research
Year(s) Of Engagement Activity 2017
 
Description Multiple presentations and posters at the World Congress of Psychiatric Genetics in Glasgow 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Our group had several presentations at the 2018 WCPG meeting, disseminating results from our work into the genomics of schizophrenia. There was considerable interest in our data and we interacted with collaborators on the projects.
Year(s) Of Engagement Activity 2018
URL https://wcpg2018.org
 
Description Presentation on long-read genomics: 2016 Workshop on Genomics, Cesky Krumlov 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Workshop on Genomics was developed in response to the increasing demand for training on how to effectively analyze and manage data generated by modern sequencing technologies. The Workshop curriculum includes extensive coverage of fundamental techniques required of all studies utilizing modern sequence data. This includes management and modification of modern sequence data files, using the Unix command-line and editors to manipulate large data files, assembly and best practices for sequence data generation, management and analysis. The second-half of the Workshop is devoted to specific sub-disciplines within the genomic sciences. While these topics may change from year-to-year, efforts are made to devote significant amounts of time to techniques being used widely in the field (e.g. transcriptomics, genome assembly, metagenomics, population genomics).
Year(s) Of Engagement Activity 2016
URL http://evomics.org/workshops/workshop-on-genomics/2016-workshop-on-genomics-cesky-krumlov/
 
Description Presentations at the Wellcome Trust Genomics of Brain Disorders Meeting, Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact We had a series of presentations - oral talks and posters - presented on our work at this international meeting on the genomics of brain disorders.
Year(s) Of Engagement Activity 2018
URL https://coursesandconferences.wellcomegenomecampus.org/our-events/genomics-of-brain-disorders-2018/
 
Description Seminar at OHSU in Portland, USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I was invited to give a seminar at OHSU in Portland where I discussed our work to medics and researchers. I discussed ongoing research into psychiatric epigenetics and established several new collaborations.
Year(s) Of Engagement Activity 2018
 
Description Symposium at 13th World Congress of Biological Psychiatry, Copenhagen 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Professor Mill was co-chair and a presenter at the ISBP meeting.
Year(s) Of Engagement Activity 2017
URL http://www.wfsbp-congress.org/former-congresses/highlights2017.html
 
Description Training seminars in genomics / bioinfotrmatics 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact The Bioinformatics Support Service (EXBiSS) offers a number of advanced training courses aimed at developing the skills necessary to handle large scale high-throughput datasets from sequencing, mass-spectrometry and ecology.
The course are available to PhD students, post-doctoral researchers and staff. As part of the current MRC funded grant, we established training in genomics and sequencing analysis.
Year(s) Of Engagement Activity 2015,2016
URL http://www.exeter.ac.uk/biomedicalhub/training/
 
Description Two selected oral presentations at the Wellcome Trust Epigenomics of Common Diseases meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact We had two platforms presenting work from this project at the Wellcome Trust Epigenomics of Common Diseases meeting.
Year(s) Of Engagement Activity 2016
URL https://coursesandconferences.wellcomegenomecampus.org/events/item.aspx?e=594
 
Description UK Pharmacogenetics and Stratified Medicine - Open Meeting - Invited Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Professor Mill gave an invited lecture on how epigenetic epidemiology might inform pharmacokinetic studies. There was considerable interest and many questions.
Year(s) Of Engagement Activity 2017
URL http://www.uk-pgx-stratmed.co.uk
 
Description Workshop on Schizophrenia and Related Disorders - Cold Spring Harbor 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I taught on the Cold Spring Harbor Schizophrenia Workshop as an invited lecturer. This involved small-group teaching to leading postdocs and PhD students selected form around the world. The students were enthused about genomics in schizophrenia and there was very positive feedback.
Year(s) Of Engagement Activity 2018
URL http://meetings.cshl.edu/schizophrenia18
 
Description XXV World Congress of Psychiatric Genetics, Orlando 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact We had multiple presentations at the 2017 WCPG meeting. We networked extensively with collaborators and established several new projects.
Year(s) Of Engagement Activity 2017
URL https://wcpg2017.org