Under a recent £23 million ($35.7 million) grant from the UK's Biotechnology and Biological Sciences Research Council, the Roslin Institute at the University of Edinburgh will focus on sequencing farm animals and the pathogens that target them.
The BBSRC recently announced the continued funding of the Roslin Institute along with seven other UK institutes as part of a broader five-year £250 million ($392 million) investment in the biosciences (GWDN 5/24/2012). Included in that funding was the Norwich-based Genome Analysis Center, which is using next-gen sequencing to study agriculturally important crops and animals, as well as bacteria (IS 6/5/2012).
The Roslin Institute is equipped with Illumina's HiSeq 2000 and Genome Analyzer. Mick Watson, director of the institute's Centre for Comparative and Functional Genomics, also called ARK-Genomics, told In Sequence that the majority of the institute's work is in functional genomics, including RNA-seq, ChIP-seq, bisulfite sequencing, methylation sequencing, and microRNA-seq.
"We're interested in using sequencing for functional genomics," he said, "in delving into the biology of the different systems."
For instance, he said, one project the institute is working on in collaboration with the Institute for Animal Health in the UK now involves sequencing of avian oncogenic viruses. For that, the scientists are using "RNA-seq to look at gene expression, ChIP-seq to look at transcription factor binding, microRNA-seq to look at which microRNAs are being expressed, and we're doing epigenetic sequencing — both methyl sequencing and bisulfite sequencing," he said.
The ultimate goal is to figure out how the viruses work and then use this knowledge to design vaccines.
As such, Roslin's needs are slightly different from other sequencing centers. For example, turnaround time is not important, he said. "We're not a diagnostics lab, so it doesn't matter whether we get results in 10 days or 10 minutes."
He said the main criteria when considering a new sequencer are accuracy, throughput, and, to some extent, read length.
Throughput is important because farm animals tend to have genomes between one and three gigabases in size. So, while an instrument like Pacific Biosciences' RS may be interesting because of its long read lengths, Watson said that its throughput is currently too low for the center's needs.
The institute primarily uses the HiSeq because of its flexibility, and the 100 base paired reads of the HiSeq are "great for most things," he said, but "if someone starts talking about 10 kilobase or 100 kilobase reads, we're obviously interested."
Reads of that length are "game changing," he said, and would "enable much finer detail for looking at structural variation."
Watson said that he is interested in upcoming sequencing technologies such as Life Technologies' Ion Proton and Oxford Nanopore's system.
Other projects underway at Roslin's ARK-Genomics include the use of sequencing to help understand disease resistance, which will enable farmers to design strategies to "keep their flocks or cattle disease free," Watson said.
There are also projects that focus on maximizing production traits such as the quality of the meat or milk yield, and even to improve animal welfare.
Aside from sequencing, Watson said the institute also uses SNP genotyping chips and gene expression chips. For many applications, SNP chips in particular are more cost-effective than sequencing for now, though he noted that "when the costs make sense, it will all be replaced by sequencing."