Sarah Sims & Jonathan Davies, Wellcome Trust Sanger Institute
Meera - This week I’m at the Wellcome Trust Sanger Institute in Hinxton, Cambridgeshire, where DNA sequencing and analysis occur on a huge scale, to help us understand just what out genes do and how they function. This one place sequenced 1/3 of the 25,000-gene human genome. But how did they do it?
In order to have genes ready to be sequenced, you need to insert the genes into a bacterium, for which you already know the DNA sequence. You place this gene insert between a part of the sequence that encodes colour, for example blue colouring, that way when the bacterium multiplies to produce colonies, the bacteria containing your insert will be disrupted in this colouring and remain colourless. This allows you to pick them out from the blue bacterial colonies that don’t have your gene insert.
So you then pick out your colonies, break open the cells of the bacteria, extract the DNA and load it onto the machines to be sequenced. But as smooth as that sounds, the stages, such as picking the colonies, can be tedious and time-consuming and can also differ depending on the opinion of the people choosing the colonies. The solution? Get a robot to do this for you!
The robots that pick colonies are basically a big box, in which there’s a tray at the bottom to put lots of petri dishes in and a robotic arm that hangs down from the top and seems to slide around. But how on earth does this box actually pick specific colonies of bacteria?
I’m off to meet Sarah Sims who’s going to fill me in on just how these robots do their job…
Sarah - Well there’s a camera that looks at each of the petri dishes, which have colonies on them, and it can see the colonies. Its been programmed to look at a certain size of colony, whether it’s a single colony and what colour it is, because there are two types of colony on there. There’s q colony with and insert and one without an insert, and the one without an insert is blue and the robot is able to identify that and doesn’t pick blue colonies, just picks the colonies that have the insert.
Meera - Just in the time that I’ve been in here now how many colonies would you say have been picked?
Sarah - Well it picks about 2000 colonies an hour. Before robots we used to pick about 800 colonies, compared to 2000.
Meera - That’s a really big difference…
Sarah - Yes it is. It’s made a huge difference with the amount of throughput we can do.
Meera - So, I know that when it comes to picking colonies you need really sterile conditions, because it’s so easy for things to get contaminated. How is that managed with robots?
Sarah - Well the room that we’re in is in sterile conditions with the air filtered, and also the robots are enclosed in a glass box, which helps prevent any air getting in to contaminate things.
Meera - I don’t think I need to say that you’re very happy about the introduction of robots?
Sarah - Yeah…yes. With the numbers we have to produce we wouldn’t be able to do it without an awful lot more people and an awful lot more lab space.
Meera - So having learned just what a difference robots have made here at the Sanger Institute, I want to know just how they work and how the were designed in the first place. So I’m here with, Jonathan Davies, who’s project manager on the robotic team.
Hi Jonathan, you design the robots do you?
Jonathan - Yes, we look at what the people in the labs want to do and then we try and design a robot that’ll cope with the tasks that they want to perform.
Meera - Did you design the colony picking ones or the pipetting ones that I’ve happened to see this morning?
Jonathan - Yes, they were designed by this group.
Meera - What was actually involved in coming up with the designs for these robots?
Jonathan - There was quite a lot of work to do with camera imaging, and looking at colonies. When they pick them by hand, you use a lot of judgement with you own eye and your own hand, but making the robot make those judgements as well, took quite a bit of fine tuning to get it right.
Meera - Would you say the robots are more accurate than the samples being done manually?
Jonathan - I think what’s more important is that they do the same task again and again, with the same accuracy. With a person doing it, sometimes you get it spot on, other times it’s not quite, but with a robot doing it you get the same result time after time after time. That’s usually what’s wanted.
Meera - These robots have made a big impact on work here at the Sanger Institute. What’s next, what are the future prospects?
Jonathan - We’re trying to come up with robots that are a lot more flexible. The ones you’ve seen where ones designed for one job and they do one job only. They do it very well, but people want to do different tasks depending on what results they get, they may want to change the robot to do it. So they want to add a bit of intelligence if you like, so we’re trying to go down that route.
Meera - But is there any risk in developing robots like that, that you might be pushing aside actually people in the labs?
Jonathan - The decisions that these humans make, they’re in no way as clever as a human being, they can only make pretty limited decisions to be honest. They haven’t got the intuition that a human being has got, which is what you need to get new results and things moving forward.
Meera - It looks like this is only the beginning of robot use in gene sequencing, but I don’t think this is a case where robots are going to take over the role of humans. Robotics is merely taking away the drudgery of lab work, allowing teams to spend time on more complicated procedures and theories, and preventing them from getting things like repetitive strain injury…
I wonder if I can get them to design a robot to do my typing for me…