Noninvasive prenatal testing: an overview

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Hi. And welcome to this Australian Prescriber podcast, where we're talking about noninvasive prenatal testing [NIPT]. I'm Dr Justin Coleman, a GP in Aboriginal health at Inala in Brisbane. And I have with me a guest who knows far more about these sorts of things than I ever will, and that is Alice Poulton. Alice Poulton is a genetic counsellor and co-author of Noninvasive prenatal testing: an overview. Which is an article, of course, in Australian Prescriber. Welcome to our humble little podcast, Alice.

Thank you so much for having me, Justin.

It's a pleasure. By way of background, so [a] noninvasive prenatal test is essentially a maternal blood test taken at or soon after 10 weeks gestation. And it looks for genetic components, as opposed to a serum blood test, which measure levels of things. This is looking for some of the DNA that has come from the fetal cells and into the maternal circulation. It separates them out through brilliant modern technology, and analyses the chromosomes of the fetal DNA.

Alice, the first thing to note is this is only one of the forms of testing we can do out there. In fact, there are a couple of others, and the others are subsidised currently by Medicare, and NIPT [noninvasive prenatal testing] is not?

Yeah. That's right. So there are three main options of aneuploidy screening for pregnant people. One is NIPT. So NIPT, you can do from 10 weeks onwards, there's no upper limit as to how late you can do NIPT. It isn't subsidised by Medicare, so it costs between 500 to $800, depending on what platform you choose. The other options are the serum screening options. So one is combined first trimester serum screening, which is done as a blood test between 9 and 14 weeks, and then an ultrasound between 11 and 13 weeks. And those statistics are combined to present you with a chance of having a child with an aneuploidy. And that's about 30 to $40 out of pocket after Medicare. And then there's second trimester serum screening, which is entirely covered by Medicare, and that's done between 14 and 21 weeks gestation.

Thank you. And I take it that it is recommended that even using NIPT, noninvasive prenatal testing, that you do do a 12 or 13 week ultrasound as well. It just adds to the information, is that right?

Yeah. That's exactly right. So NIPT is not perfect, and it's a chance that they might miss something. An ultrasound really just helps as another method of screening, to check the things the NIPT could miss.

And what are we looking for, mainly with NIPT? I know that the science of genetics is expanding rapidly. And no doubt, there are hundreds if not more things we could be looking for. But I take it it's usually done for the fetal aneuploidies, the trisomies, is that right?

Yeah, that's exactly right. So every single NIPT platform is really good at picking up the 3 most common aneuploidies, so that's trisomy 21, which is Down syndrome, trisomy 13, which is Patau syndrome, and trisomy 18, which is Edwards syndrome. But there are different platforms that can offer more screening as well. So they look across other aneuploidies, whether that's rare autosomal aneuploidies, so extra or missing copies of chromosomes that aren't chromosomes 21, 18, 13, or the sex chromosomes. They can look for sex chromosome changes. And some platforms also look for micro-duplications or deletions. So small regions of chromosomes that might be missing or extra.

We'll cover the pros and cons of each. I guess there's no single recommended choice for these things, it's all about informed patient choice. But when these things first came out, the general most common usage, which perhaps remains the most common usage, is decisions around a termination of pregnancy. And part of the timing, of course, is to make a termination viable. But there are other benefits as well.

Yeah, absolutely. And I think a big reason a lot of people use it is to find out the sex of their baby.

Yes.

But you're absolutely right. I think originally when we were offering screening, a lot of people presumed it would be because people would act on the results of screening outcomes. But I think there's a growing recognition, that actually screening information can be really helpful to help people prepare for the birth of a child who might have additional needs. An alternative in some cases when we have a false positive result, it could still have relevance for the placenta, and so might give us information about needing extra ultrasounds as the person continues on in the pregnancy. So there is definitely utility of this sort of screening beyond people making decisions around continuing or ending a pregnancy.

So it's not merely an expensive way, a 500 to $800 add-on to your gender reveal party?

Exactly.

Make sure you pick the right colour balloons.

Yeah.

Well, let's talk about once a patient has been informed of the cost and the benefits. Let's look at what the result means. It is important to note that all these 3 tests you mentioned are screening tests rather than diagnostic tests. Although, the sensitivity and specificity of the tests do mean, I believe, that a positive result in an NIPT is potentially more significant than a positive result in the other tests, is that right?

It really just depends on what chromosome condition there's a high chance result for. So for things like Down syndrome, NIPT is really good for. It's also quite good for Edwards syndrome, so trisomy 18, and Patau syndrome, trisomy 13. It's less accurate for some of those other chromosome changes that we'll discuss a little bit later. But it does outperform the serum screening for trisomy 21 or Down syndrome.

Because for the serum screening, I'm used to getting a result that sort of puts a ballpark figure, saying it's high risk, as in more than one in 100 chance, for example. Although, it does become more specific than that. If you have a positive test for trisomy 21, for example, NIPT, it really is a very strong indicator that the baby does have trisomy 21.

Yeah, that's exactly right. So normally if we get a high chance result on NIPT, we'd be presuming that over 99% of the time, that result will go on to be confirmed, versus serum screening, you're correct, normally you'll get a result that's under one in 300 is the quoted chance.

Part of the information we supply the patient with before they even consider having the test in the first place is of course what they might do if the result comes back positive. Because these are screening tests, the most common outcome of a positive result for any of these things would be getting confirmatory invasive diagnostic testing.

Yeah. And that's something we definitely recommend for people, even though we're quite confident with NIPT results particularly for Down syndrome. It still is a screening test, and so we recommend individuals confirm using either CVS [chorionic villus sampling] or amniocentesis.

In this burgeoning genetic tests market, there are many providers. In general, NIPT can currently be divided into targeted screening for higher prevalence conditions, and a broader net fishing for a wider range of chromosomal abnormalities. How do you compare those 2 approaches, Alice?

Yeah. So neither is better than the other. They're really just different. They're both using different NIPT methods, which is why one will be able to look at some things and the other one can't, and vice versa. When we're talking about the genome wide, that really involves looking across all of the chromosomes. It can tell us information about the common chromosome changes, like I mentioned before. The sex chromosome changes. But it also looks across all of the other chromosomes and checks to see if there are any extra or missing ones, as well as big chunks of chromosomes that might be extra or missing.

What it isn't able to do is it isn't able to look at really small changes. So it can look for changes that are about as big as what you'd be able to see under a microscope on a karyotype. But it can't look for changes that are smaller than that. Whereas the targeted screening doesn't look across every single chromosome, it really just looks at those more common chromosome changes, sex chromosome changes. And then it looks at a select numbers of regions that we see more common chromosome changes in. So there's micro-duplications and micro-deletions. 22q syndrome might be one that some listeners are familiar with. And we'll perform targeted screenings to look for changes in those particular regions.

So for a health provider making a recommendation of one or the other to a woman who's pregnant, what sort of factors do you take in consideration? There'd be cost differences. I assume there are more false positive differences with the broader net?

Yeah, that's exactly right. So there can be cost differences, depending on what platform you're looking at. Some platforms offer a more basic level of screening, where they're only looking at common autosomal aneuploidies, versus an add-on where you look at a greater number. But for some, they just routinely include genome wide and they look across every single chromosome. So it's important to look at what the provider you're offering offers.

You're correct in that the broader we pass the net, the more likely we are to get false positives. And where we often see false positives are for things like rare autosomal aneuploidies. So that's for chromosomes that aren't 13, 18, 21, or the sex chromosomes. Generally though, an entire extra copy of one of those chromosomes would lead to an early pregnancy loss. They're really rarely observed at birth, and they're very rarely observed even at 10 weeks gestation. So generally, if we're getting a higher chance screening result for one of those conditions, more likely than not, it's confined to the placenta and isn't in the baby itself.

And so that's one limitation of genome wide screening, is that it can pick up these things that raise anxiety in the pregnant person, and they go on to be confirmed as a false positive. And like I mentioned before, sometimes that can have utility of if we know that there's a chromosome change in the placenta, or presume there's one in the placenta, it might encourage us to do additional growth scans later on in the pregnancy.

And as part of the informed consent, I guess it is always important to mention the procedure-related risk of these 2 types of invasive testing. Can you give us an outline of that?

Yeah, absolutely. So chorionic villus sampling, CVS. And that's the test that we can do from 11 weeks gestation, generally between 11 and 14 weeks gestation, and that has a procedure-related risk of one in 500. Amniocentesis is done a little bit later on in the pregnancy, so it's done from 15 and a half weeks onwards. And that has a procedure-related miscarriage risk of one in 1000.

So clearly, a lot of information to give this informed consent. It's not going to be a quick little conversation. Is there any particular genetic information, genetic screening information resource you recommend?

So a really good resource for pregnant people, or people who are planning a pregnancy and want to learn more abut their screening options is the decision-aid, which is hosted by the Murdoch Children's Research Institute. And it's just a stepwise resource that people can use to work out what their preferences might be in terms of accessing prenatal screening. And there are also good resources available on a lot of the NIPT provider websites. So depending on what platform you provide, it's worth having a look at their website and what they provide, to give a little bit more information on their type of screening.

Looking at the result now of the NIPT, the result is one of 3; positive, negative, or no-call or a failed result?

Yeah, that's right. So you'd either get a high chance result, a low chance result, or an inconclusive or no-call result.

Tell me about the inconclusive result. Where does that leave the provider and the woman? What decisions do they have to make then?

Yeah. So when we get a no-call or an inconclusive or a failed NIPT result, it just means that the test wasn't able to provide a result. And the most common reason for that is that there just wasn't enough of that fetal DNA in the sample for them to give an accurate result, or a result that they felt confident in. And so the amount of placental DNA that's in the maternal bloodstream can vary due to a number of factors. So one is gestational age. And that's why we tell people to have the test done after 10 weeks. Before 10 weeks, there's generally not enough placental DNA to get an accurate test. So sometimes, people just waiting a couple of weeks, particularly if they haven't had an accurate dating scan, they're going off their last menstrual period, that can be a solution to getting a result.

Maternal weight can also play a role. So someone with a high BMI might have a lower fraction of placental DNA in their bloodstream, so that can be another reason we get an inconclusive result. And there are also maternal medical conditions that can contribute to being a no result. And generally, consent forms will ask about those conditions. But I guess another thing you should be mindful of is a low amount of placental cell-free DNA in a maternal bloodstream can also be associated with fetal aneuploidy. And so if we're getting consistent no results for someone, generally about 50% of the time they do a redraw you'll be able to get a result. But if you fall into the 50% where we're not able to get a result, just important that their patient is counselled on the slightly increased chance of aneuploidy and have diagnostic testing options presented to them as well.

So with a failed result, a common path would be to repeat the test. And then by the sound of it, really, if it's another inconclusive test, a lot of women would probably go onto invasive testing at that point?

Yeah. Look, we present it to people as an option. It really depends on the person and what their risk perceptions are. Some people might be happy with having a serum screening test as another option. Some might be happy with having ultrasound alone. And we just offer them diagnostic testing if they wanted definitive confirmation on that fetal carrier chart.

Well, Alice Poulton, you have very clearly outlined noninvasive prenatal testing. I know far more than I did 15 minutes ago about it. Thanks so much for coming on the podcast.

Thank you so much for having me.

Alice Poulton has been employed by the Monash IVF Group, which owns one particular noninvasive prenatal testing brand. And her PhD was funded by the Monash IVF Group, University of Melbourne, and the Murdoch Children's Research Institute. My guest’s views are their own, and don't represent Australian Prescriber. And my views are certainly all mine.