This article has been updated from a previous version with additional information.
The UK's Medical Research Council said yesterday that it has granted more than £7 million ($10.7 million) in funding to create three new high-throughput sequencing hubs in England and Scotland.
Separately, the UK's Biotechnology and Biological Sciences Research Council said yesterday that together with the MRC, it has invested £1.65 million ($2.5 million) in a new sequencing facility at one of its research institutes near Cambridge that will be a partner of one of the three new MRC hubs.
The announcements come a little over a month after the BBSRC said it is opening a new sequencing center, the Genome Analysis Centre, in the Norwich Research Park in June, funded with £13.5 million from the BBSRC and a number of regional and local agencies (see In Sequence 4/7/2008).
The new MRC and BBSRC funding helps increase both the number and capacity of next-generation sequencing facilities in the UK, the largest of which is currently the Wellcome Trust Sanger Institute, with almost 40 Illumina Genome Analyzers, several 454 GS FLX instruments,and a number of legacy Sanger instruments installed.
The MRC said that it is now "boosting the UK research community's access to cutting-edge equipment for DNA sequencing by making a substantial investment in the latest technology."
It has given the three regional centers funding to purchase high-throughput sequencing instruments, which they will make available to academic groups across the UK.
Eastern Sequencing and Informatics Hub
The Eastern Sequencing and Informatics Hub in the East of England involves the University of Cambridge, the European Bioinformatics Institute, the Babraham Institute, and the National Institute for Health Research Cambridge Biomedical Research Centre. It received £2.4 million, or about a third of the MRC funding, and has a focus on medical sequencing.
The center, headed by Principal Investigator John Todd, a professor at the Cambridge Institute for Medical Research at the University of Cambridge, will be based at Addenbrooke's Hospital in Cambridge.
At present, the hub only has traditional capillary sequencing instrumentation, Todd told In Sequence by e-mail, but it plans to acquire at least two different second-generation sequencing platforms. "We want a diverse tech base since we have so many applications to cater for," he said.
The hub has an ongoing collaboration with 454 Life Sciences and Applied Biosystems, to which the companies are contributing discounts, early access to technology, know-how, and their own researchers, according to Todd.
In addition, the EBI will contribute "in a major way" to computing and data storage for the hub, he said.
According to the MRC, the EASIH has "a research development and strategic aim to apply high-throughput sequencing to routine medical diagnostic uses, in particular HLA typing in transplantation and cord blood stem cells, prenatal diagnosis, and resequencing of disease genes," such as the BRCA genes, in collaboration with the National Blood Service and the National Health Service's Regional Clinical Genetics Services. In collaboration with the EBI, the hub will also "provide researchers with access to all the tools required to analyze these complicated datasets."
Todd said the aim is to "test the utility and possible cost benefits of high-throughput sequencing for [National Health Service] genetic clinics."
Earlier this year, Todd and his colleagues, in collaboration with Roche's 454 Life Sciences, published a study in Science in which they resequenced 10 candidate genes from genome-wide association studies that were implicated in type 1 diabetes in 500 samples and controls, using 454's sequencing technology, and found a number of mutations in one of these genes (see GenomeWeb Daily News 3/5/2009).
The Babraham Institute, a BBSRC research institute outside of Cambridge, said in a separate announcement last week that it has built its own sequencing facility, funded with £1.65 million ($2.5 million) from the BBSRC and the MRC, "in partnership" with the University of Cambridge's Centre for Trophoblast Research. The Babraham facility will be a partner of the Eastern Sequencing and Informatics Hub and will focus on epigenomic research.
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The North of England
The North of England hub consists of the University of Liverpool, the University of Sheffield, the University of Manchester, and the University of Lancaster and is headed by Neil Hall, a professor at the school of biological sciences at Liverpool. It has received £2 million from the MRC and £200,000 million from the Northwest Regional Development Agency.
The hub will expand the capacity of the existing Advanced Genomics Facility at the university, which Hall, a former assistant investigator at the Institute for Genome Research and project leader at the Wellcome Trust Sanger Institute, founded two years ago with a single 454 Genome Sequencer (see In Sequence 7/17/2007).
The facility is currently equipped with two Applied Biosystems SOLiD 3 systems and two 454 GS FLX sequencers, according to Hall. The new funding will allow him to add two more instruments, but he has not yet decided which ones, "as this would be driven by the planned science."
The center will support projects in cancer research, genetic susceptibility, and personalized medicine, and will be supported by the Clatterbridge Cancer Research Trust, which has so far provided £150,000. More funding from the trust will be available for cancer sequencing, Hall told In Sequence by e-mail.
Planned projects include "some major studies" with local groups of lung and pancreatic cancer, he said. The hub is also partnering with a center for personalized medicine to search for rare variant mutations that are linked to negative drug responses.
The Scottish hub involves the University of Edinburgh, the University of Dundee, the MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine, the University of Glasgow, the University of Aberdeen, and the Roslin Institute of the University of Edinburgh.
The center, headed by Mark Blaxter, a professor at the Institute of Evolutionary Biology of the University of Edinburgh, received about a third of the £7 million funding, which it will use to build on existing capacity at GenePool, a next-generation sequencing and bioinformatics facility at the University of Edinburgh.
At present, GenePool is equipped with a 454 GS FLX Titanium, an Illumina GA II, and several Applied Biosystems 3730 sequencers, Blaxter told In Sequence via e-mail, and will be adding "additional short-read and long-read instrumentation" as part of the expansion.
In addition, the hub will "seed the establishment" of research bioinformatics positions at the five partner universities and institutes "to assist investigators in the analysis of the torrents of new data that will be produced," according to the MRC.
GenePool will serve researchers studying the genetics of cardiovascular disease, psychiatric disorders and cancer, genetics of early development, and the pathology and epidemiology of infectious diseases.
According to Blaxter, projects will include the sequencing of malaria parasites from patients and from genetic crossing, targeted resequencing in human psychiatric disorders, sequencing of community-circulating strains in pathogenic bacteria, and resequencing of mouse genomes.