Video transcript: The Genome Analysis Centre

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October 2012

Professor Jane Rogers, Director, The Genome Analysis Centre (TGAC)
The Genome Analysis Centre has been established to exploit the very high throughput sequencing that is now possible of DNA, to analyse both the structures of genomes and how they are used. So, we're interested in their function and that is combined with bioinformatics, both computing capacity and a large team of skilled people.

Video shows some of TGACs genome analysis equipment.

The Genome Analysis Centre is one of the most advanced centres in the world with respect to the types of equipment that we're using. We have a good range of different DNA sequencing technologies so that we can mix and match them for our purposes.

Video shows Matthew Clark walking around TGAC's equipment room.

Dr Matthew Clark, Team Leader, The Genome Analysis Centre
This is our equipment room where we keep all of our sequencers. It is very noisy in here because we have to have a lot of air conditioning. The machines produce a lot of heat, they all have their own fans, and we have to pump the heat away.

This is a MySeq. This is one of my favourite machines. It's an Illumina machine. We have a lot of larger Illumina machines, but the advantage of this one, although it gives us less data, it actually gives us the data much more quickly and because I work in sequencing technology development, this allows me to do experiments and get the answers quickly and then move onto doing the next experiment having based that on the answers that I get. And it uses a very small flow cells and has a simple cartridge system that basically has everything that these two things just plug in, and we can give it the samples. And the advantage of this is that instead of taking ten, eleven days to give us a result, we can get a result within a single day.

Professor Jane Rogers
The high throughput DNA sequencing capacity and the high capacity of computing that TGAC has are a national capability and that means that we are a unique resource for the bioscience community within the UK.

Video show Matthew Clark demonstrating the Pacific Biosciences RS.

Dr Matthew Clark
This is the Pacific Biosciences RS. This is one of our most recent machines. It is a very loud machine. Most of our machines are quite loud because we have to control very carefully the climate conditions inside them. The advantage of this machine, which is quite large, is that it actually gives us very, very long reads. Inside here we get very small chips, like this one, which this single chip has 150,000 miniscule little wells which are only nanometres across and each of those wells holds a single piece of DNA and a single enzyme. And using the lasers and specialised optics in this machine, we can actually look at each piece of DNA being sequenced in real time. So we can see the different nucleotides being added by the polymerase because each of the nucleotides have a different dye attached to it. And that is happening as we actually look at the screen, we can see them coming up.

It is very interesting technology for us because it allows us to sequence thousands, maybe even tens of thousands of bases from a single piece of DNA, which is much longer than what we can get with other technologies. The other thing that it allows us to do is to look at the native DNA, there is no arification involved, it is directly the DNA that comes from the organism that we're sequencing. So, we can actually look at slight modifications on the DNA, which is a field called epigenetics, so we can look at things like just little methyl groups, CH3, which is attached to particular nucleotides. And those are very important in turning particular genes on and off. And we can look at that natively using this platform.

Professor Jane Rogers
The Genome Analysis Centre is special because the wide range of organisms that we're working on and the different types of analysis that we're undertaking. So very often we're asked to develop a strategy to solve a problem and to develop analysis modules and tools that can be used for many other experiments in the future.

Video shows TGAC researchers working on the wheat genome.

So one of the things that we're doing at the moment is working on the wheat genome. The wheat genome is a very complex genome. It's hexaploid and sequencing it is not straight forward. So we're taking an approach where we are sequencing individual chromosomes and developing tools to compare and contrast the sequences that we can generate from each of the individual chromosomes.

Video shows biochip.

Dr Matthew Clark
This is a biochip that allows us to look at the quality of the nucleic acids that are being sent in by our collaborators. So we only need to put one or two microlitres of sample in here but that allows us to look at incredible detail at both the size and the quantity of the amount of material that they're sending us and whether it is useful and appropriate to make a whole library out of it. So we can just put one or two microlitres in here, and this does eleven different samples, and load it into our bioanalyser and run it. And within a few minutes we'll get the results.

Professor Jane Rogers
Over two thirds of the people in The Genome Analysis Centre are involved in bioinformatics analysis. So that's taking the sequence data that we generate, processing it, managing it, and then undertaking different types of analysis. So we have the BBSRC high-strategic aims of food security, bioenergy, and healthy living. And the work that TGAC does actually spans all of those areas and increasingly we're looking at how we can use informatics as a focus for developing new models that can be applied in these different areas of focus.



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