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Q&A: Jane Rogers on Expanding the UK's Sequencing Prowess Beyond the Sanger Institute and Medical Research


JaneRogersPhoto.jpgName: Jane Rogers
Title: Director, the Genome Analysis Centre, Norwich Research Park, UK
Experience and Education:
Scientific administrator, later head of sequencing and member of the board of management, the Sanger Centre/Wellcome Trust Sanger Institute, 1993-2007
Scientific administrator, Medical Research Council, 1990-1993
Research associate, University of Cambridge
PhD in biochemistry, University of Southampton
BSc in physiology and biochemistry, University of Southampton

Previously the head of sequencing at the Wellcome Trust Sanger Institute, Jane Rogers is now directing a new sequencing center in the UK, the Genome Analysis Centre, or TGAC, that is slated to open its doors in Norwich next month.

With £13.5 million ($20.5 million) in funding from the Biotechnology and Biological Sciences Research Council and local authorities in the East of England, the center plans to become "a world-class national facility for the study and application of genomics in animals, plants, and microbes," according to its website.

Last week, the Medical Research Council announced that it is investing more than £7 million in three additional high-throughput sequencing centers in England and Scotland (see article in this week's issue)

In Sequence spoke with Rogers about her new enterprise earlier this month at the Biology of Genomes meeting at Cold Spring Harbor Laboratory.

Can you provide some background information about the Genome Analysis Centre, and how it came about?

The Genome Analysis Centre came about as a result of increasing recognition of the value of genomics research, and resources in biological research, and a lack of any substantial genomics facility in the UK outside the Sanger Institute to contribute to generating these resources. It will focus on non-medical research.

Genomics is now considered to be key to several initiatives that the BBSRC wishes to pursue, especially its new strategies towards food security, living with environmental change, and stimulating applications of mathematical biology.

The centre is located on the Norwich Research Park. It occupies a building that was built about seven years ago, originally to house a joint genomics facility that was to be shared between the John Innes Centre, [a research center for plant science and microbiology,] and Syngenta. The space is designed for genomics work and has not been fully utilized until now because Syngenta [which resulted from a merger of Novartis Agribusiness and Zeneca Agrochemicals in 2000] moved their genomics operations to San Diego several years ago.

How many people will be working at TGAC?

We initially intend to employ around 40 people. We can see that rising to 60 to 70, and the staff will be supplemented by graduate students, visiting workers, et cetera.

We also hope to develop programs with industry where we can facilitate the development of new skills and training.

How will you be equipped with sequencing instrumentation?

We plan to install a few capillary sequencers and then to build up next-generation sequencers and computing facilities.

The projects that we are going to be looking to deliver on will be genome references for organisms that are key to the scientific programs and have not yet been sequenced. It will include plants but also plant pathogens, fungi, and bacteria, as well as microbes that occupy different ecosystems.

To deliver the reference genomes, we will still make some use of Applied Biosystems 3730 capillary sequencers, especially for generating end-sequences of clones for scaffolding. The Sanger Institute is actually facilitating setting up those technologies in Norwich.

And then we are looking to install a mixture of the next-gen platforms that are available now. We expect to install six instruments in the first instance; then, we will build on that base, depending on what the requirements are, and the performance of the instruments.

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Are you also keeping an eye on so-called "third generation" sequencing technologies?

Yes, very much so. We are very interested in the developments with Oxford Nanopore Technologies, and also Pacific Biosciences.

I think they could offer ways of reducing cost even further, and potentially being able to generate longer read lengths, which always helps with haplotype analysis, and of course with genome assembly — and I'm anticipating having to assemble several new genomes.

In addition, we will be doing a lot of genome-transcriptome comparisons, and also metagenomics and metatranscriptomics.

Can you mention a few projects you are currently considering?

I hope that we can contribute to the completion of the tomato genome. That's actually a project that I was involved in when I was still at the Sanger Institute, where we were sequencing chromosome 4 as part of an international consortium that is sequencing the tomato.

There may also be some additional work to do on Medicago truncatula and comparative legume projects.

A major challenge for the future is going to be the crop genomes relevant to the UK. Wheat is the biggest one, and there is an international consortium looking at mapping and sequencing the wheat genome. There are groups here in the UK who are really involved in that, and we hope to work with them. For example, the BBSRC is funding a whole-genome shotgun sequencing project of wheat, which is being carried out in Liverpool at the moment. It's a SNP discovery project, though, not a genome project.

What are the biggest challenges with the types of projects you will be tackling?

I think the biggest challenge is developing resources that are useful for breeders. One of the major challenges with many crops is that the genome resources are not very substantial, and breeders need reliable markers, preferably where they understand the biology behind the marker. And I think developing those, and working with breeders to deliver what they need, is going to be a major challenge. By working closely with the researchers who are trying to understand specific traits, we can hopefully deliver something applied and useful.

Are you also planning to work with crop companies?

If we can develop partnerships, yes, we would like to do that. We are certainly looking for opportunities to work with both large and small companies.

What about bioinformatics — how much of your resources are you devoting to that?

Probably 50 percent of the capital costs for equipment will be computing equipment. And to begin with, about 50 percent of the staff are planned to be bioinformatics staff, and we see that growing.

We are taking the bioinformatics challenges very seriously. The BBSRC held a workshop fairly recently about the challenges of large datasets, and obviously, next-generation sequencing is just one of the types of data that is posing a challenge. I think we will be looking into options such as the use of cloud computing and shared resources for storage, and also, there will be a need to develop new solutions for data transfer. That's a major issue.

How is TGAC funded?

We have estimated that the capital required for the first five years would be around £13.5 million, and that funding provision is being shared by BBSRC, the East of England Development Agency, and Norwich and Norfolk local authorities.

EEDA and the local authorities are very keen to see genomics initiatives stimulate new types of enterprise and innovation in the Norwich area. Three scientific institutes, scientific departments within the University of East Anglia, and the Norwich and Norfolk University Hospital are co-located on the Norwich Research Park and we are working together to develop a scientific strategy that will build on the existing strengths in plant, food, and environmental research in Norwich.

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