How to study a phenome

How do we study phenomics?
12 November 2019

Interview with 

Elaine Holmes, Sam Lodge, Australian National Phenome Centre


A woman with her back to the camera in a lab, using scientific equipment


Phenomics involves tracking the levels of thousands of chemicals in the body to spot patterns that can predict diseases a person is at risk from. So how will these measurements be made? Elaine Holmes is an analytical chemist helping to lead the initiative at the new Australian National Phenome Centre. She took Chris Smith through how samples will be processed in the lab, including visits to researcher Sam Lodge…

Elaine - Here we are in the first stop on our sample journey. What you can see is a room, it's about your average size of a living room, and it's full of large magnets. And these magnets look... if you can imagine a giant tea urn. So each of these big tea urns contain greater than the whole of the Earth's magnetic field within the can. And so if you think in terms of the big magnets that would pull your car upwards in a scrap heap, this is way, way more powerful than those.

Chris - And that has the effect of doing what to the sample is it as it goes down inside the can?

Elaine - Well the magnetic field is pretty strong, and there are some chemicals, some atoms, that have a property we call spin. So they're like little bar magnets and they're spinning. And when you put them into a magnetic field they start to line up with the field. And if you then shoot some energy in, a radio frequency pulse, it makes these little bar magnets flip; and then as they relax again back to their relaxed position, if you like, they're emitting energy, and you pick this up. And because every chemical has different atoms, they interact with the magnetic field in a slightly different way. And these small differences we can pull apart and you end up with a series of peaks which we call our molecular fingerprint. This actually is a very quick technique. If you put your sample in you can have a spectrum, you can have your fingerprint, if you like, within five minutes.

Adam - So NMR, nuclear magnetic resonance, is a very speedy way to identify lots of molecules in a single sample and to do it very cheaply. But what sorts of things can the team look for? And what does the output from the machines actually look like? Sam Lodge.

Sam - So it results via a transformation into something called a spectrum, which has two axes. On the vertical axis will be intensity, so if there's something that's very concentrated, you have a high intensity. On the bottom axis is something called ppm; this is parts per million. This is the point at which it resonates.

Chris - Looking at this computer screen, this is an example of the sort of thing that the machine would generate. This looks like almost a sawtooth. So the height of each of those peaks corresponds to how much of the substance was in the sample that you put into the machine, and along the x-axis, these are all the different types of chemical that it's picking up.

Sam - Yeah, so it's a little bit more complicated than that. So each peak is essentially from a proton in a particular chemical environment. So one metabolite might have several different peaks, because you might get different compounds with different proton environments.

Chris - So how do you sort them all out then? How does… because that just looks like a really complicated sawtooth. How do you work out what chemicals that corresponds to?

Sam - We run standards, and these standards are one particular chemical, so we can get a chemical signature.

Chris - I see. So you run a bunch of known chemicals through, you know what pattern they would produce, and you just compare what comes from your sample to what you know it should look like, and then you can say, “oh, that's in there, that’s in there, that’s in there…” To give a practical example then, say the doctor puts me on antibiotics. At the moment the dose that we prescribe for people is just a standard dose for any adult. But my metabolism might be different to your metabolism, so the amount I'm taking might be different than the amount that you would actually need to take. Could you use this to work out how much antibiotic there is in my blood compared to, say, your blood, and therefore work out whether I'm metabolising it faster than yours, and therefore tailor my dose better?

Sam - Yes, you can exactly do that, because an MRI is actually quantitative. We can monitor any drug compound within a sample, measure the concentration, so essentially we can then tailor the dose to be perfect for that particular individual.

Chris - So it's not just your own body's own molecules, but you can look at things we put into our body from outside?

Sam - Yes. And it's not just drugs either. So we can look at different food compounds, so for example someone who eats a lot of meat would have a high amount of carnitine in their blood, in their urine. Someone that’s eaten a lot of fish will have a compound called TMAO, and that changes dependent on the time from consumption.

Chris - So it's almost like dietary forensics. You can work out whether someone's lying to you when they say they've eaten certain things, you can work out what they’ve really eaten and when they've eaten it.

Sam - Yes. Yes, we can pick up things like alcohol, caffeine; and every food has a different marker which we can identify, so we know exactly what someone's eaten.

Chris - If you're not actually actively looking for those things, will they nonetheless be present in these readouts so that you could go back and look for them later? If someone a researcher comes to you and says, “well actually Sam I'm doing a study on this substance in the blood,” and you happen to have screened a million people by then, could you go to your computer and just pull out a million people's worth of these traces, and look for that particular molecule that's interesting for that researcher?

Sam - Yes, you can. So the way the NMR data is actually stored is actually very powerful, because we can run something now or in five years time, and we can overlay them and compare them.

Adam - Sam Lodge. But what about the things that NMR can't tell you? Like substances present in only tiny amounts? Elaine Holmes again.

Elaine - So now we want to go a little bit deeper into the profile, find out a little bit more about what's in your sample, so we come to the second stage - which is our mass spectrometry laboratory.

Elaine - So this room's a little bit bigger, as you can see. And it's full of 16 different machines. Looks like a big box with a big stick coming out of the box. And these are all a type of mass spectrometer that we use to do screening. So we're trying to look at everything we can in your sample. We don't tell the machine, “I want to look at fats, I want to look at sugars.” We just put it in and we want to capture everything we can about the sample.

Chris - Why is this used and why is this different, or what does this do for you that we can't get out of the NMR machines next door?

Elaine - NMR machines are very reliable. So you can measure things very accurately. But it doesn't have the capacity to go to really, really low concentrations. Maybe for other diseases you want to look at your hormones, or things that are present in very tiny concentrations. And this is where mass spectrometry comes into its own.

Chris - And how do these machines work compared with what the NMR machines do?

Elaine - These machines still separate molecules out but they did in a slightly different way. So they're separated in two ways. The first is called chromatography, and that's where you put your blood sample or your urine sample onto a column, and different chemicals stick and different chemicals go straight through. And you can then run some liquid through this, and they'll start to bleed out of the column, but at a slightly different rate. And we can catch them as they come off. You can then separate them a little further by putting them into the mass spectrometer part, and this is really just a weighing machine. All you're looking at here is how much your molecule weighs and what its charge is.

Chris - How do you work out what the actual molecule is? Because if you just get a weight and you just get a charge, there are lots of different possible arrangements of atoms that could be that weight and that charge. So how do you sort them out?

Elaine - Well we have databases where we've looked at molecules, and standard molecules, chemicals you can buy, so we know what some are. But you don't always know what they are. In these cases, what you need to do is separate them even further so you've got a single chemical. And then you blast the chemical apart, you split it up and break it; and you look at the fragments, how much each little part of the molecule weighs. And like a jigsaw puzzle you pull them all back together, add all the weights up, to make sense of the whole picture.

Adam - Elaine Holmes.


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