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ARK-Genomics Using $1.8M Grant to Purchase HiSeq 2500, Automation for Livestock Genomics


This story was originally published Dec. 31, 2012.

The ARK-Genomics sequencing facility at the University of Edinburgh's Roslin Institute plans to use a recent £1.1 million ($1.78 million) grant from the UK's Biotechnology and Biological Sciences Research Council to purchase new automation tools and a HiSeq 2500 to sequence farm animal exomes, the genomes of livestock and plant pathogens, and eventually to enable population genomics of livestock.

The facility is currently equipped with one Illumina HiSeq 2000, which it recently upgraded to the 2500, and one Illumina MiSeq instrument. With the recent funding, it plans to purchase another HiSeq 2500.

The grant follows a £23 million ($35.7 million) BBSRC award that the institute received earlier this year to sequence farm animals and their pathogens (IS 6/12/2012).

Mick Watson, director of ARK-Genomics, told In Sequence that the rapid run mode of the 2500 is useful for ag-bio sequencing applications, particularly in projects where the center sequences pathogens from an outbreak on a farm, for instance.

"There's a clinical market in the veterinary side of things," he said. "When animals die, we need to know quickly what they died from." Using sequencing to "track epidemiology on a farm, is a very useful thing to do," he added.

Additionally, he said, as a sequencing service provider, sometimes customers want projects done quickly, so the 2500 enables the center to offer faster turnaround times for an increased price.

Currently, one of the main projects the center is working on is to develop exome capture kits for pig, chicken, and sheep, Watson said. The researchers are currently testing both Roche's NimbleGen and Agilent's HaloPlex technology.

While the center itself won't commercialize specific kits, Watson said that exome sequencing for those farm animals would be offered as a service and having ready-made kits would help to streamline the workflow.

One challenge in designing the kits, Watson said, is that many of the animal genomes are not fully annotated. "We've augmented [the exomes] in Ensembl, because some of the annotations are missing genes, UTRs, exons," he said.

The Roslin Institute is uniquely positioned to provide this data, Watson added, because it is housed within the University of Edinburgh's veterinary school and therefore has access to lots of DNA samples from livestock.

After augmenting the annotation data, the next step is to design the primers to enrich or capture the exome, and then test sequencing at different coverage levels to "see what we get with the initial design — how many genes are covered or missing at 20x, 30x, 40x," he said.

Once kits for pig, sheep, and chicken have been refined, Watson said that the center would like to move on to companion animals, like dog and horse.

Aside from the 2500, the center plans to purchase tools for automation, although Watson said that it has not yet decided on which equipment. "What we're really trying to do with this investment — the new HiSeq 2500 and automation — is to drive the cost of sequencing down to enable population sequencing in farm animals," he said, "so you can sequence thousands instead of hundreds of animals."

Until recently, the lab's sequencing projects consisted of tens of samples, so it was feasible to just have a person do library preparation. But now, "we're finding that's becoming a real bottleneck because people are doing hundreds of samples" in one project.

Robots to automate that portion of the workflow would help eliminate that bottleneck, he said. One project Watson said the center is interested in pursuing is a sequencing study of the neurodegenerative disease scrapie in sheep. The Roslin Institute currently maintains a flock of hundreds of sheep, half of which are susceptible to scrapie, and half of which are resistant to the disease.

"We'd love to sequence every single sheep in the flock and look at mapping the loci that may be linked to resistance to scrapie. At the minute, the cost is prohibitive, so we can't sequence whole flocks of sheep very easily or very rapidly," he said. But the investment in automation as well as the 2500 will help to drive those costs down so studies like this become feasible, he said.