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.
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.
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
MacInnes SJ
(2015)
Genetic variation in inflammatory and bone turnover pathways and risk of osteolytic responses to prosthetic materials.
in Journal of orthopaedic research : official publication of the Orthopaedic Research Society
Merga JY
(2013)
Exploring the diversity of Arcobacter butzleri from cattle in the UK using MLST and whole genome sequencing.
in PloS one
Miller FW
(2013)
Genome-wide association study of dermatomyositis reveals genetic overlap with other autoimmune disorders.
in Arthritis and rheumatism
Mitchell AL
(2014)
Association of autoimmune Addison's disease with alleles of STAT4 and GATA3 in European cohorts.
in PloS one
Moran JC
(2017)
Comparative Transcriptomics Reveals Discrete Survival Responses of S. aureus and S. epidermidis to Sapienic Acid.
in Frontiers in microbiology
Moura AE
(2015)
Phylogenomics of the killer whale indicates ecotype divergence in sympatry.
in Heredity
Mutwakil MZ
(2017)
Transcriptomic and metabolic responses of Calotropis procera to salt and drought stress.
in BMC plant biology
Narayanan RP
(2013)
IGF2 gene polymorphisms and IGF-II concentration are determinants of longitudinal weight trends in type 2 diabetes.
in Experimental and clinical endocrinology & diabetes : official journal, German Society of Endocrinology [and] German Diabetes Association
Nowell RW
(2017)
A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.
in GigaScience
Noyes HA
(2015)
A simple procedure for directly obtaining haplotype sequences of diploid genomes.
in BMC genomics
O'Brien S
(2017)
Adaptation to public goods cheats in Pseudomonas aeruginosa.
in Proceedings. Biological sciences
Ofon E
(2017)
A polymorphism in the haptoglobin, haptoglobin related protein locus is associated with risk of human sleeping sickness within Cameroonian populations.
in PLoS neglected tropical diseases
Olohan L
(2018)
A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.
in BMC genomics
Panoutsopoulou K
(2017)
Radiographic endophenotyping in hip osteoarthritis improves the precision of genetic association analysis.
in Annals of the rheumatic diseases
Payton A
(2016)
A TOMM40 poly-T variant modulates gene expression and is associated with vocabulary ability and decline in nonpathologic aging.
in Neurobiology of aging
Peters MJ
(2013)
Genome-wide association study meta-analysis of chronic widespread pain: evidence for involvement of the 5p15.2 region.
in Annals of the rheumatic diseases
Ransom-Jones E
(2017)
Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity.
in mSphere
Rodriguez-Fontenla C
(2014)
Assessment of osteoarthritis candidate genes in a meta-analysis of nine genome-wide association studies.
in Arthritis & rheumatology (Hoboken, N.J.)
Rothwell S
(2016)
Dense genotyping of immune-related loci in idiopathic inflammatory myopathies confirms HLA alleles as the strongest genetic risk factor and suggests different genetic background for major clinical subgroups.
in Annals of the rheumatic diseases
Rothwell S
(2017)
Immune-Array Analysis in Sporadic Inclusion Body Myositis Reveals HLA-DRB1 Amino Acid Heterogeneity Across the Myositis Spectrum.
in Arthritis & rheumatology (Hoboken, N.J.)
Schirmer M
(2015)
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.
in Nucleic acids research
Sniekers S
(2017)
Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence.
in Nature genetics
Sniekers S
(2017)
Erratum: Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence.
in Nature genetics
Soutter F
(2015)
Restricted dog leucocyte antigen (DLA) class II haplotypes and genotypes in Beagles.
in Veterinary journal (London, England : 1997)
Styrkarsdottir U
(2017)
Whole-genome sequencing identifies rare genotypes in COMP and CHADL associated with high risk of hip osteoarthritis.
in Nature genetics
Tachmazidou I
(2017)
Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.
in American journal of human genetics
Trampush JW
(2017)
GWAS meta-analysis reveals novel loci and genetic correlates for general cognitive function: a report from the COGENT consortium.
in Molecular psychiatry
Veltsos P
(2017)
Mating system manipulation and the evolution of sex-biased gene expression in Drosophila.
in Nature communications
Wardle R
(2017)
Identification of Equid herpesvirus 2 in tissue-engineered equine tendon.
in Wellcome open research
Wilson IW
(2019)
Genetic Diversity and Gene Family Expansions in Members of the Genus Entamoeba.
in Genome biology and evolution
Description | Membership of BBSRC Transformative technology Panel |
Geographic Reach | National |
Policy Influence Type | Membership of a guideline committee |
Impact | The transformative technology strategy advisory panel have influence BBSRC policy on data intensive bioscience and big ideas pipeline |
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 |