Centre for Genomic Research: Genomics Hub Renewal

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

Abstract

Over the last 5 years molecular biology has been transformed by the application of new sequencing technologies. These technologies allow DNA and RNA to be sequenced much faster than was previously possible and at a significantly reduced cost. These developments create opportunities for researchers working within the MRC remit. Hence, the MRC funded four sequencing hubs in recognition of this in 2009, one of which is the Liverpool Centre for Genomic Research (CGR).

The CGR has a number of different income streams. It receives funding from the MRC and the Natural and Environmental Research Council (NERC), via its Biomolecular Analysis Facility, to provide collaborative services to groups working within the respective remits. The facility has also benefited from support by the University of Liverpool for staff salaries and equipment purchases. The CGR also as generates income by re-charging project costs from academic collaborators or commercial clients. In addition, the CGR co-directors hold a number of grants and hence the CGR is both a research lab and a service lab. We will make the service operation of the CGR become financially self-sustaining over the next 3 years by recharging the full cost to collaborators and clients.

This application seeks funding for a further two years but at a substantially reduced rate that will complete the transition of the CGR to financial self-sustainability. To enable this evolution, the CGR will continue its current work but also put in place a number of new initiatives.
1. We will expand and develop the equipment in the CGR to keep up with advances in throughput and cost.
2. We will focus on expanding our market reach by hiring a Business Manager.
3. We will present a number of training events aimed at the MRC research community to inform biomedical researchers on genomic technologies, analytical methods and applications of high-throughput sequencing data.
4. To expand our reach into the MRC research community we will offer a second pump-priming competition to allow MRC-linked applicants to undertake trial or technology development projects within the CGR facility at minimal cost.

Technical Summary

The CGR has acted as one of the MRC DNA-sequencing hubs for two years and in that time has tripled its turnover, significantly increased its laboratory workflow and sequencing capacity, developed higher throughput pipelines, implemented LIMS as well as instigating software and hardware solutions. In that time, it has also completed 394 sequencing and array projects for the UK community, with its user base currently including 75 Universities/Research Institutes and 17 groups working in the commercial sector. The CGR has a current staff of 19 persons and currently runs six different sequencing platforms: Ion Torrent PGM; 454 FLX+ and 454Jr; ABs SOLiD v4 and 5500xl; and the Illumina GAIIx. The CGR is completing the purchase of two Illumina HiSeq2000s. The CGR is aimed primarily at providing a service for small-to-medium sized projects to the UK research community. This proposal requests two additional years of reduced funding to allow the CGR to further to expand its market and complete the move to a fully self-sustainable business model. To achieve this, we request funds to (i) hire a Business Manager to drive a vigorous marketing campaign, (ii) run a training and outreach activities to encourage more research users and (iii) develop research projects with some of the largest research initiatives in the North of England. The CGR will also engage in a number of large collaborative research proposals that will ensure the CGR maintains an academic and research-led philosophy.

Planned Impact

The Centre for Genomic Research is works with a vast variety of different research fields and collaborates with researchers in all biomedical fields as well as researchers working in basic biology and environmental science. The CGRs key strengths are in genome sequencing, genomic technology and bioinformatics and we aim to make an impact from our research through the following methods:

1. Working with the The University of Liverpool Business Gateway to identify potential areas for commercial exploitation of the work we do. We will also embed a business manager within the CGR who will take responsibility for this
2. Outreach to the research community, the medical community and the general public through formal and informal presentations, marketing material and social media.
3. Training of researchers through targeted training events in collaboration with other MRC hubs and CGAT.

We aim encourage all members of staff to be actively involved in these activities.

Researchers working with the CGR will get the benefit of having trained staff assigned to their project as well as access to cutting edge equipment. They will also have advice of experienced scientists in the design of their project. This will reduce costs and increase the chances of success of for these researchers and we will therefore have an impact on many different disciplines in biomedical sciences and the research councils and charities that fund them.

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. This will raise the awareness of scientists and non scientists about genomic technology.

The CGR also benefits industry by providing a complete service for contract sequencing and bioinformatics. This raises the competitiveness of UK companies and therefore helps retain employment within the UK.

Publications

10 25 50

publication icon
Baird AE (2014) Genetic basis of cranial cruciate ligament rupture (CCLR) in dogs. in Connective tissue research

publication icon
Balaskas P (2017) MicroRNA Profiling in Cartilage Ageing. in International journal of genomics

 
Description BBSRC responsive mode
Amount £433,798 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2011 
End 03/2013
 
Title DNA sequence data 
Description Every week we generate >10gb DNA sequence from range of samples provided by collaborating groups. This can be from human/plants/microbes or animals. 
Type Of Material Database/Collection of Data/Biological Samples 
Year Produced 2006 
Provided To Others? Yes  
Impact Our data has been used to develop new tools such as Pyronoyes (Quince et al) and RY mapper (Ashelford et al). It has fed into databases such as EUPAthDB. 
 
Description Bioinformatics training 
Organisation University of Edinburgh
Department Edinburgh Hub for Trials Methodology Research
Country United Kingdom 
Sector Academic/University 
PI Contribution We are collaborating with the MRC hub for Scotland in training delivery
Collaborator Contribution We will share a training bioinformatican post to deliver joint workshops
Impact We are currently hireing
Start Year 2012
 
Description Collaborations with Unilever 
Organisation Unilever
Department Unilever UK R&D Centre Port Sunlight
Country United Kingdom 
Sector Private 
PI Contribution Genome data generation to underpin programs in personal and home care divisions of Unilever.
Collaborator Contribution Provision of materials.
Impact Better understanding within Unilever of microbial communities as relevant to personal and home care.
Start Year 2013
 
Description H3 Africa 
Organisation University of Glasgow
Country United Kingdom 
Sector Academic/University 
PI Contribution We will be sequeincng and genotyping large numbers of human samples over the next two year in a WT/NIH consortium
Collaborator Contribution Sample collection
Impact Project just started
Start Year 2012
 
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