Establishing a single cell genomics facility

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology

Abstract

Genomics, which is the study of the entire DNA content of a cell, has radically changed our understanding of biological systems as it can be used to identify all of the genes in any particular organism. We can use this information to predict how biological systems function and then test these hypotheses through further experimentation. Transcriptomics is a sub-branch of the field of genomics. This involves the study of all of the RNA in a cell and can be used to identify what genes are active in any particular environment.
However, until recently it has not been possible to analyse genomes and transcriptomes in single cells, as the techniques required use large amounts of DNA, hence most of our current knowledge is taken from large groups of cells from tissues or cell culture. Also, some microbes that can't be cultured or isolated in large numbers have not been studied at all.
However, new methods that enable uniform amplification of nucleic acids have been developed and experiments can now be directed individual cells, and early studies have demonstrated that cell populations can be extreme heterogeneous at the DNA and RNA level and we need to measure this heterogeneity to properly understand the underlying biology.
In order to perform single cell genomic experiments we will develop a dedicated clean lab with a suite of tools for isolating single cells and rapidly processing nucleic acids for genomic and transcriptomic analysis. The lab will be adjacent to, an operated by, the Liverpool Centre for Genomic Research. One of the UKs most advanced DNA sequencing laboratories.
This proposal is collaboration between six research active universities and four national facilities for genomic sequencing and analysis. We aim to make the facility open-access to all researchers in the UK through a pay for access system which will allow reinvestment in equipment and will cover staff support.

Technical Summary

It is becoming well established that heterogeneity of genomes and transcriptomes at the single cell level is responsible for the emergent phenotypes at the multicellular level. Studying this heterogeneity at the single cell level has, in the past, been severely hampered by our ability to take measurements of DNA or RNA sequence at such limiting quantities of template. However new technologies such as MALBAC amplification, rolling circle amplification and transposon based library construction techniques have made single cell genomics a feasible approach. However, due to the requirement for hyper-clean DNA-free environments and specialist cell isolation instruments for preparing material, it is not a simple approach.
In this project we will refurbish and equip a dedicated single cell genomic analysis lab. The lab will have dedicated air filtering and positive pressure and will house state the art single cell isolation technologies; cell sorting and microfluidics. Along with automated cell lysis, and library preparation systems.
The lab will be run by and adjacent to the Center for genomic research but will be a joint venture with the Liverpool Centre for Cell Imaging, the Birmingham MicrobesNG group and Edinburgh Genomics and will access capability in all groups.
The lab will be open-access and available as a pay-for-use service. We also plan a number of training and outreach activities to engage the community in the use of single cell genomic techniques

Planned Impact

We propose explicit outreach and training activities to bring information on the capabilities and capacity available through the Centre for Genomic Research to potential users and other stakeholders. We aim to make an impact from our research through:
1. Assisting collaborators in pump-priming work, in designing experiments, in applying for funding and in publishing their results, depositing data in public repositories, and exploiting commercial potential of findings. Researchers working with the CGR and Edinburgh Genomics will get the benefit of having trained staff handle their project and having access to cutting edge equipment. We will therefore have an impact on many different disciplines in basic and applied sciences and on the research councils and charities that fund them.
2. Working with The University of Liverpool's Business Gateway to identify potential areas for commercial exploitation of the work handled though the CGR. We also have embedded a project/business manager within the CGR to drive this area forward.
2. Reaching out to the research community and the general public through formal and informal presentations, marketing material and social media. In this, we will utilise the effective press communications systems within the University of Liverpool to communicate our work to wider audiences, and use public forums such as open days, social media and our website to further publicise our work (NL writes one of the most popular blogs in the field of genomic technology) . The CGR is also part of a wider UK community of academic service laboratories with whom we co-organise the annual UK Genome Science Meeting, to ensure the relevance and reach of what the CGR offers as a facility.
3. Training of researchers in the applications of next generation sequencing through targeted training events in collaboration with our partners in Scotland with whom we share the post of an MRC funded training bioinformatician. There is a recognized skills gap in next generation sequencing training provision. The CGR is committed to running at least three annual training courses and - in collaboration with Edinburgh Genomics - will run Master classes and residential summer schools as of mid 2015, coordinated and delivered by a dedicated training bioinformatician: (1) Master classes, aimed at researchers of all seniorities and delivering an overview of the technologies, their applications, the core algorithmic underpinnings of next-generation genomics analysis, as well as hands-on experience in using some of the analytical tools. (2) Residential Summer Schools, focused on reaching the coming generation of researchers: PhD students, postdoctoral researchers and early career fellows and lecturers. They will include hands on experience of next generation sequencing, in depth training in the key analytical technologies, and a programme of lectures on applications from guest lecturers and specialists. The aim is for these events to become self-funding by 2015.
4. Encouraging all CGR staff and staff associated with research grants led by the Investigators to be actively involved in these activities. In addition, the CGR is active in training PhD students and postdocs. There are 6 PhD students working within the CGR and we run numerous courses and give presentations on our science internally and externally.
5. Working closely with the technology platform providers to drive innovation and test new methodologies and applications. The CGR has a close working relationship with Roche, Illumina and Agilent, acting as a reference site and certified service provider for applications. We will also continue to host manufacturer-led seminars as events aimed at providing networking opportunities between academics and commercial partners.
6. Benefiting industry by providing a complete service for contract sequencing and bioinformatics. This raises the competitiveness of UK companies and therefore helps employment within the UK.

Publications

10 25 50
 
Description We have isolated and sequenced endosymbionts of an important agricultural pest.
Exploitation Route this information could be sed as targets for novel insecticides.
Sectors Agriculture, Food and Drink

 
Description Materials Innovation factory 
Organisation Unilever
Department Unilever UK R&D Centre Port Sunlight
Country United Kingdom 
Sector Private 
PI Contribution We are partners in a open innovation space
Collaborator Contribution Unilever are co-locating personell and contributing to equipment and building costs
Impact none
Start Year 2012
 
Description PHE HPRU 
Organisation Public Health England
Country United Kingdom 
Sector Public 
PI Contribution The CGR is a key part of the sequencing capability for Public Health Protection research unit. Part of the CGR
Collaborator Contribution They have provided samples and expertise which have allowed our group to be part of publications and to develop piplines and analyses for other projects.
Impact Several papers on the analysis of west african ebola
Start Year 2014
 
Description School visits 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Numerous school visits to the CGR
Year(s) Of Engagement Activity 2015,2016