A new core facility at the University of Liverpool is betting that next-generation sequencing will enable it to offer large amounts of genomics data without having to become a genome center.
A few weeks ago, the new Advanced Genomics Facility, which is part of the university’s school of biological sciences, installed a 454 GS FLX — its first instrument, which will also remain its only sequencer for the time being.
“It’s a very good time to move this sort of technology into a university setting because these new machines allow you to do genomics without the genome center,” said Neil Hall, a professor in the school of biological sciences who directs the facility.
Some of the first applications the facility will offer are de novo sequencing of bacterial genomes, comparative sequencing, BAC sequencing, deep PCR sequencing for SNP detection, metagenomics, and cDNA sequencing for expression analysis, according to its website.
Hall returned to his alma mater in April after spending three years as an assistant investigator at the Institute for Genome Research and four years as a project leader at the Wellcome Trust Sanger Institute.
With funding from the university and the UK’s National Environment Research Council to start a genomics facility, he acquired the sequencer, making the University of Liverpool one of the first British schools to own the tool. The University of Newcastle Upon Tyne is the only other UK university Hall knows of that has decided to buy a 454 sequencer.
Two full-time technicians will run the instrument, and Hall is in the process of hiring two bioinformaticians to manage and analyze the sequencing data, which will also include developing new algorithms.
The reason Hall chose 454’s sequencer over Illumina’s is that at the time he was looking, “more people were testing it, so we knew what it could do.” Also, the longer reads of the 454 platform are more suitable for de novo sequencing, he said, an application requested by several researchers at the University of Liverpool who are working on species other than model organisms, where the genome sequence is not known.
Hall spent a lot of time getting the informatics infrastructure in place before the sequencer was installed. “Unless you have got that right, the machine isn’t going to be of much use to you,” he said. This included hiring the bioinformatics staff, ensuring access to compute clusters at the university’s computer sciences department, and purchasing a high-end Dell server for doing assemblies, and implementing systms for regular data backups.
“It’s a very good time to move this sort of technology into a university setting because these new machines allow you to do genomics without the genome center.”
“I think that’s probably the hardest part,” he said. “The machine you can get from the company, and they show you how to use it, and it comes with kits and guides, whereas the informatics is more complex.”
The sequencer will be available to researchers both inside and outside of the university, either as part of collaborations or on a fee-for-service basis.
Hall has already seen a lot of interest in his new core, which he said is one of the few that provides sequencing to all researchers, not only those focused on medically relevant projects.
The Wellcome Trust Sanger Institute, on the other hand, focuses on medical research, he said. “Since we said we are getting this machine and people could use it, we have been inundated with requests.”
In his own research, which is funded by the Royal Society, Hall plans to use the instrument for comparative sequencing and expression studies of parasites such as Plasmodium, Trypanosoma, and Entamoeba in order to find genes involved in virulence and host specificity.