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
D'Amore R
(2016)
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling.
in BMC genomics
Davies G
(2014)
A genome-wide association study implicates the APOE locus in nonpathological cognitive ageing.
in Molecular psychiatry
Nowell RW
(2017)
A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.
in GigaScience
Olohan L
(2018)
A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.
in BMC genomics
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
Adams SE
(2017)
A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology.
in Scientific reports
Noyes HA
(2015)
A simple procedure for directly obtaining haplotype sequences of diploid genomes.
in BMC genomics
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
O'Brien S
(2017)
Adaptation to public goods cheats in Pseudomonas aeruginosa.
in Proceedings. Biological sciences
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.)
Mitchell AL
(2014)
Association of autoimmune Addison's disease with alleles of STAT4 and GATA3 in European cohorts.
in PloS one
Daly K
(2016)
Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus.
in Environmental microbiology
Bronowski C
(2017)
Campylobacter jejuni transcriptome changes during loss of culturability in water.
in PloS one
Ahouty B
(2017)
Candidate genes-based investigation of susceptibility to Human African Trypanosomiasis in Côte d'Ivoire.
in PLoS neglected tropical diseases
Moran JC
(2017)
Comparative Transcriptomics Reveals Discrete Survival Responses of S. aureus and S. epidermidis to Sapienic Acid.
in Frontiers in microbiology
Alt DP
(2015)
Complete Genome Sequence of Leptospira interrogans Serovar Bratislava, Strain PigK151.
in Genome announcements
Kelly J
(2017)
Composition and diversity of mucosa-associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences.
in Environmental microbiology
Ilott NE
(2015)
Corrigendum: Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes.
in Nature communications
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
Daly K
(2014)
Dietary supplementation with lactose or artificial sweetener enhances swine gut Lactobacillus population abundance.
in The British journal of nutrition
Dowall S
(2014)
Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity
in Genome Biology
Cornick JE
(2017)
Epidemiological and Molecular Characterization of an Invasive Group A Streptococcus emm32.2 Outbreak.
in Journal of clinical microbiology
Sniekers S
(2017)
Erratum: Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence.
in Nature genetics
Hackinger S
(2017)
Evaluation of shared genetic aetiology between osteoarthritis and bone mineral density identifies SMAD3 as a novel osteoarthritis risk locus.
in Human molecular genetics
Elliott KS
(2013)
Evaluation of the genetic overlap between osteoarthritis with body mass index and height using genome-wide association scan data.
in Annals of the rheumatic diseases
Merga JY
(2013)
Exploring the diversity of Arcobacter butzleri from cattle in the UK using MLST and whole genome sequencing.
in PloS one
Baird AE
(2014)
Genetic basis of cranial cruciate ligament rupture (CCLR) in dogs.
in Connective tissue research
Wilson IW
(2019)
Genetic Diversity and Gene Family Expansions in Members of the Genus Entamoeba.
in Genome biology and evolution
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
International Glossina Genome Initiative
(2014)
Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.
in Science (New York, N.Y.)
Sniekers S
(2017)
Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence.
in Nature genetics
Baird AE
(2014)
Genome-wide association study identifies genomic regions of association for cruciate ligament rupture in Newfoundland dogs.
in Animal genetics
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
Miller FW
(2013)
Genome-wide association study of dermatomyositis reveals genetic overlap with other autoimmune disorders.
in Arthritis and rheumatism
Carr DF
(2017)
Genome-wide association study of nevirapine hypersensitivity in a sub-Saharan African HIV-infected population.
in The Journal of antimicrobial chemotherapy
Howrigan DP
(2016)
Genome-wide autozygosity is associated with lower general cognitive ability.
in Molecular psychiatry
Joshi PK
(2017)
Genome-wide meta-analysis associates HLA-DQA1/DRB1 and LPA and lifestyle factors with human longevity.
in Nature communications
Leckenby A
(2015)
Genomic changes during evolution of animal parasitism in eukaryotes
in Current Opinion in Genetics & Development
Gaither MR
(2018)
Genomics of habitat choice and adaptive evolution in a deep-sea fish.
in Nature ecology & evolution
Jani M
(2014)
Genotyping of immune-related genetic variants identifies TYK2 as a novel associated locus for idiopathic inflammatory myopathies.
in Annals of the rheumatic diseases
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
Christoforou A
(2014)
GWAS-based pathway analysis differentiates between fluid and crystallized intelligence.
in Genes, brain, and behavior
Clarke A
(2017)
Heightened autoantibody immune response to citrullinated calreticulin in bronchiectasis: Implications for rheumatoid arthritis.
in The international journal of biochemistry & cell biology
Wardle R
(2017)
Identification of Equid herpesvirus 2 in tissue-engineered equine tendon.
in Wellcome open research
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
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 |