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ARK-Genomics and GenePool Form Edinburgh Genomics to Handle Increasing NGS Demands


Two genomics facilities within the University of Edinburgh, GenePool and ARK-Genomics, have merged to form Edinburgh Genomics, which will offer next-generation sequencing services, bioinformatics, and genotyping.

The center is equipped with six Illumina HiSeq 2500 machines and three Illumina MiSeq systems, and will receive support from the Medical Research Council, the Natural Environment Research Council, and the Biotechnology and Biological Sciences Research Council.

Mark Blaxter, professor of evolutionary genomics at the University of Edinburgh will serve as director of Edinburgh Genomics. Karim Gharbi, who was previously the scientific manager of GenePool, will serve as head of genomics, while Mick Watson, previously the director of ARK-Genomics, will be head of bioinformatics.

Watson told In Sequence that the two entities decided to merge to cope with the increasing size of projects researchers were requesting, frequently on the order of a 1,000 exomes or transcriptomes, Watson said.

"You can't do 1,000 exomes with one HiSeq," he said. "That was one of the main reasons for us to merge and become a bigger facility."

Previously, ARK-Genomics had focused on livestock genomics, sequencing farm animal exomes, as well as livestock and plant pathogens.

However, projects at Edinburgh Genomics will span the entire field of biology, Watson said, including livestock, plant and animal genomics, metagenomics, and human genomics and translational science. This is in part due to the fact that Edinburgh Genomics will receive funding not only from the BBSRC, but also the MRC and NERC.

The center does not have plans to obtain CLIA certification, Watson said, as that is not something that its customers and partners have requested.

He also said that the most common request has been exome sequencing, primarily because researchers increasingly want to sequence thousands of samples, and exome sequencing is more cost efficient than whole-genome sequencing for studying large sample sizes.

Watson said that while the center's R&D team will evaluate existing and new sequencing technologies, in the near term he does not anticipate bringing on an alternative to Illumina's sequencing technology.

He said that the center would consider purchasing Ion Torrent technology if Life Technologies' new chemistry, Hi-Q, reduces errors in homopolymer regions as the company claims it will. Additionally, he said that the center has applied to Oxford Nanopore's early access program for the MinIon and is also interested in working with Illumina's Moleculo technology for long reads. Illumina launched the Moleculo technology as a service in July and plans to introduce kits by early next year.

Watson added that the genomics center is also using Illumina's TruSeq kits for library preparation and is evaluating the Nextera kits, especially Nextera's mate pair kit and exome kit, and hopes to validate those to run at a production level.

Watson said that the new facility will compete with existing sequencing service organizations such as BGI both in terms of price and also by providing more than just "sequencing grunt." Aside from the technical aspects of sequencing services, he said the facility has a lot of research expertise in each of its core areas of human genetics, livestock and plant genomics, and metagenomics.

Going forward, he said that one of the main hurdles for next-gen sequencing is making sense of the data. The issue is more than just the sheer number of reads that next-gen systems produce, he said. Because projects now often involve hundreds or even thousands of samples, even after the data is processed there are still thousands of "predictive SNPs across the exomes." Taking that information and figuring out what it means is still a barrier, Watson said.

He added that he thinks interesting solutions will be developed as the technology is used more clinically. On the research side, organizations can employ more bioinformaticians, but "what's really going to be interesting" are companies in the clinical space that come up with software that can take the information and "present it in a way that physicians can understand it and are interested in it."