High throughput Sequencing Hub for the North of England

Lead Research Organisation: University of Liverpool
Department Name: Sch of Biological Sciences

Abstract

DNA sequence has always been an important source of inspiration for advances in medical and clinical research. This culminated in the sequencing of the first human genome, a project that took 6-8 years and several billion pounds. As a result we were able to discover the number and identity of genes that defined the human form though it is taking much longer to work out how these genes interact. But we know that people vary from each other in their disease susceptibility or in the way that they respond to treatment. The current need is to understand the basis of this variation and to use it to understand more fully how to define the most appropriate treatment to particular patients presenting with a particular condition. This is called ?personalised medicine? and it is widely thought to be the best way of optimising treatment.
Achieving this requires establishing the DNA sequence of particular genes in those patients, and this requires much more productive sequencing technologies. Fortunately, new instruments are now becoming available which can sequence a human in just a few weeks for approx #10-50,000. The Advanced Genomics Facility (AGF), located in Liverpool, is a leading UK centre of excellence and service provider for the new generation of sequencing technologies. We want to expand the capacity of the AGF to serve the research leaders in Universities and hospitals of the North of England by offering a one-stop shop that provides advice for all stages of the work. We shall also provide training and pump-prime cost-sharing programmes helping client groups to turn DNA sequence into knowledge.

Technical Summary

The North of England has substantial amounts of class-leading medical and clinical research based in major Universities and NHS Trusts, all of which would benefit greatly from access to second generation (2G) DNA sequencing technology, particularly in meeting the challenges of tumour sequencing, genetic susceptibility and personalised medicine. The Advanced Genomics Facility (AGF), located in Liverpool, is a leading UK centre of excellence and service provider for nextgen sequencing. We propose to expand the capacity of the AGF to serve the MRC-related interests in the Universities and NHS Trusts in a consortium covering Liverpool (lead), Manchester, Sheffield, and Lancaster. We shall provide expert access to all three major second generation (2G) technologies, to informatic processing and analysis techniques, and in the medium-term to third generation (3G) technologies. We shall provide training and pump-prime cost-sharing programmes helping client groups to turn DNA sequence into knowledge. Important points in the favour of the AGF include: a strong track record of servicing academic clients; a leading edge position in genome science and sequencing technology; an experienced workforce; minimised consumables costs; multiple platforms; expert informatics capability; a mature open door policy on research collaboration; a training and translation strategy; close working relationships with 2G technology providers including discussions with a 3G provider; and excellent links into the regional and nextgen sequencing communities.

Publications

10 25 50
 
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 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 NHS PhD fellowship Julie Sibbering 
Organisation Liverpool Womens NHS Foundation Trust
Department Liverpool Women's Hospital
Country United Kingdom 
Sector Hospitals 
PI Contribution We are hosting an NHS research Fellow. Julie Sibbering was working in the clinical diagnostics lab at the liverpool womens hostpital and was awarded the fellowship to work in my lab of Next-gen sequencing methods to identify chromosome abnormalities.
Collaborator Contribution Julie Sibbering brings expertise in clinical diagnostics to the group.
Impact Funding from NHS for fellowship. Training for the student.
Start Year 2009
 
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 teacher training 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Primary Audience Schools
Results and Impact A group of teachers from a local school came for CPD training in modern biological techniques. They received presentation and hands on experience using genomic technology

The school reported this was the best CPD they ever had.
Year(s) Of Engagement Activity 2010