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UK's TGAC Eyes New Sequencing Technology; Focuses on De Novo Assembly of AgBio Species, Microbes

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This article was originally published May 31.

Equipped with an array of next-gen sequencers and flush with a recent £19 million ($30 million) investment from the Biotechnology and Biological Sciences Research Council, the Genome Analysis Center in the UK is planning sequencing and assembly projects focused on agriculturally important plants and animals, as well as bacteria.

The center currently has three Illumina HiSeq 2000s, one Genome Analyzer, three MiSeqs, two of Roche's 454 GS FLX systems, one Pacific Biosciences RS, and OpGen's Argus Whole Genome Mapping system.

Jane Rogers, director of TGAC, said that the center would be investing in platforms that keep it competitive in the field. The goal is not to ramp up its sequencing capacity per se, but to "enable us to remain state of the art in next-generation sequencing," she added.

Going forward, she said she is keeping a close eye on new technologies, such as Oxford Nanopore, is considering upgrading at least one HiSeq 2000 instrument to the 2500, and is reviewing Life Technologies' Ion Torrent platforms, both the PGM and the Proton.

Additionally, she said that the center is investing in computing to increase its storage capacity and computing power to undertake large de novo assemblies.

The bulk of the center's sequencing is done on the Illumina HiSeqs, which she said are used to "generate a lot of sequence coverage."

The center is increasingly using the PacBio RS to help improve assembly after initial sequencing. TGAC researchers are also investigating how to use the OpGen system to improve assembly.

"The error rate [of the PacBio] is high, so reads need correcting, but the ability to generate long reads is helpful," Rogers said. "And the absence of bias is useful" for "more even coverage."

The OpGen system is brand new — the center has had it for less than three weeks — so the researchers are still figuring out how to use that system and in what applications it could be most useful.

The MiSeq is being used primarily for technical development projects and for bacterial sequencing projects, while the 454 is used for amplicon sequencing and cDNA sequencing.

Rogers said that the center plans to get the MiSeq upgrades that Illumina will launch mid-year. New capabilities for the system — including 2x250 reads and increased throughput — would potentially enable the MiSeq to take over the work that is currently being done on the 454, she said.

"The extent to which we continue to use [454] will depend on whether the other platforms take over those roles," she said. The MiSeq upgrades will "be a challenge for the 454."

Rogers said that the center is increasingly doing more de novo assembly, particularly of bacteria genomes. She said she expects those projects to increase as well as projects looking at "genome variation in different varieties of crops and diversity amongst crops."

The center does a mix of its own internal projects as well as collaborations with university researchers and other BBSRC institutes like the John Innes Center and the Institute of Food Research, both of which are located in the Norwich Research Park where TGAC is headquartered.

Most of the center's academic collaborations are with researchers without next-gen sequencing capabilities, and especially without bioinformatics expertise, which Rogers said is a very important part of TGAC's services.

Currently, TGAC does not have a clinical focus and Rogers said that the center has not looked into becoming certified to offer clinical services. However, both the University of East Anglia and the Norfolk and Norwich University Hospital are located at the Norwich Research Park, and Rogers said she expects to work more closely with these institutions in the future. The hospital, in particular, is expanding its research portfolio, she said.

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