We review common genetic tests available for diagnosis of chromosomal anomalies: karyotype, FISH, and microarray. We are joined by Angela Scheuerle, MD, Professor of Pediatric Genetics at the University of Texas Southwestern Medical Center.
Dr. Neeta Goli:
Welcome to Newborn News, a podcast where we discuss educational topics from medical professionals who care for newborns. I'm your host, Dr. Neeta Goli, a pediatrician in the UT Southwestern newborn nursery. Welcome back to the podcast. In today's episode, we'll be discussing genetic testing. We're recording remotely due to the ongoing COVID pandemic. We are joined today by Dr. Angela Scheuerle, Professor of Pediatric Genetics at UT Southwestern.
Dr. Angela Scheuerle:
Hello.
Dr. Neeta Goli:
Hi, Dr. Scheuerle, thanks for joining us today.
Dr. Angela Scheuerle:
You're very welcome. Thank you for inviting me.
Dr. Neeta Goli:
So if we examine a baby in the newborn nursery who has findings that are suspicious for a chromosomal abnormality, there are many different tests available for us to order. Today we'll learn about each of them and which test is appropriate in any given clinical scenario. But before we discuss all the genetic testing specifically, Dr. Scheuerle, please can you give us a brief refresher about normal chromosome count and some types of chromosomal anomalies we might encounter?
Dr. Angela Scheuerle:
Sure. So let me answer that the way I would explain it to a patient's family, okay. Remembering that when I'm talking to a patient, I usually have pictures in front of me. So human beings have 46 chromosomes and they come in pairs and the pairs are numbered largest to smallest, 1 to 22. Girls have two X chromosomes and boys have an X and a Y and that makes us boys and girls, or more accurately, the SRY gene on the Y chromosome makes boys and everybody else is girls. The most important part is that there needs to be a normal amount of DNA. Sometimes it's rearranged like in a balanced translocation, but if there's no net gain or loss, you're okay. It's still normal in terms of the amount of DNA that's available.
Dr. Angela Scheuerle:
It's possible to have an extra or missing copy of really any of the chromosomes. It's believed that trisomy 16 is really thought to be the most common trisomy, but complete trisomy 16 never results in a viable fetus. It always miscarries very early. The trisomies that we see most commonly in the babies, which are the 13, 18, and 21, are believe it or not actually the least severe of the trisomies. And I know that can be a hard thing to get your head around, but these are the ones that are viable enough to survive to delivery. And even given that, the majority of all fetuses conceived with those, including 13, 18, and 21, will miscarry. We estimate that less than half of the fetuses conceived with trisomy 21 will make it all the way to delivery. Of the missing chromosomes, the most common is the 45,X Turner Syndrome, in which their second sex chromosome is missing.
Dr. Angela Scheuerle:
And then there are conditions caused by missing or extra parts of a chromosome. Most people learn about Cri-du-chat in medical school. It's caused by missing the top end, the distal P arm, of chromosome number five. And then the most common of these small copy number variants is the 22q11.2 deletion and that may be as common as one out of every 3,000 babies. And this is a small section of one of the smallest chromosomes that's missing.
Dr. Neeta Goli:
So what are some of the most common physical exam findings in a baby which might raise concern for us for chromosomal abnormalities?
Dr. Angela Scheuerle:
Okay, well, the short answer is it would be multiple congenital anomalies involving two or more organ systems or regions of the body. And we would count growth failure as an anomaly. Small size, or realistically, unexplained gross overgrowth is the same, counts as a birth defect in this situation. The longer answer is more complex and sort of boils down to the gestalt of the child. The story I tell is that when I was in training, Dr. Frank Greenberg, who was the geneticist who trained me, would walk out of a patient's room and say, "Oh, well that looked chromosomal." And I would say, "Okay, good. Tell me what you're seeing that makes you say that." And he'd say, "Well, because that's what it looks like." And while you can see how that wasn't the most helpful answer, but after a while, you sort of get a hang of what you're looking at.
Dr. Neeta Goli:
So when should we consult you all in pediatric genetics for input?
Dr. Angela Scheuerle:
Well, ideally as soon as there's a concern about growth, structural, or functional anomalies in the baby, hopefully before any genetic testing is ordered or at least before it's sent, even if ordered by or suggested by another group. If there's no question about the diagnosis and all you need is confirmation, we can usually help facilitate the testing, including insurance checks, which can be tricky. We can also help make sure that the best version of the test gets sent and that we avoid redundancy in testing. Genetic testing is expensive and even the fastest tests take a few days. So we sometimes have inside information that will speed up the test or save some costs.
Dr. Neeta Goli:
So what are the different tests that are available to us?
Dr. Angela Scheuerle:
Well today we're talking about chromosome problems. So within that context, there are three common tests, the routine karyotype, the chromosome microarray, and the fluorescence in situ hybridization, or FISH testing.
Dr. Neeta Goli:
So when is it appropriate for us to order each of these tests?
Dr. Angela Scheuerle:
I'm glad you asked it because this is an important question. So routine karyotype is for babies who clinically have one of the big aneuploidies, trisomy 13, 18, 21, Turner syndrome, something like that. It is often not necessary to send FISH testing if the clinical picture is a whole chromosome problem. And there are two reasons for that. The first is that FISH testing is incomplete. And regardless of when you send it for any reason, you're always going to need to do a karyotype anyway. So you're always going to end up doing two tests. FISH testing tell us what's going on at a single point on the chromosome. That one point can be normal while most of the rest of the chromosome is abnormal.
Dr. Angela Scheuerle:
And an easy example for me, chromosome 13. On chromosome 13, the locus for the FISH probe is the retinoblastoma gene, which is just under the centromere. And I've seen more than one baby have a normal trisomy FISH screen, including two apparently normal copies of chromosome 13, who then turn out to be missing most of the rest of the long arm of the chromosome. The other reason that FISH needs to be accompanied by karyotype is for recurrence risk counseling. We need to know whether the baby has a free trisomy or a translocation. Translocations in trisomy 21, for example, happen about 10% of the time and finding that means further testing of the parents and more involved counseling and so we need to know that. So you're always going to end up doing a karyotype in addition to FISH.
Dr. Angela Scheuerle:
Routine karyotype is also important if we're worried about chromosomal mosaicism, the presence of two or more types of cells in the body. The lab can look at many cells, typically a couple of 100 is standardization and determine whether there's a significant frequency of normal versus abnormal. And if we're looking for mosaicism, it's important that the lab know you're asking that question. Otherwise, they're going to do the standard number of cells.
Dr. Angela Scheuerle:
So the obvious question that always get asked is how do you do this and how do you deal with this if you're making withhold/withdraw decisions about the baby? And the answer to that in my recommendation would be to order a stat karyotype. The UT Southwestern Veripath lab can turn around a stat full karyotype in about the time it takes to do a FISH test, which is 48 to 72 hours and that's without the added time to ship a sample to another city. That particular test is more expensive, but it's not as expensive as a karyotype and trisomy FISH together. So you get all the answers you need quickly and less expensively. Now, certainly there are times where even two to three days is too long and interphase FISH testing that's done without waiting for the cells to divide technically can be done in a couple of hours. You get the sample, you run through it, and you can get the answer in a couple of hours. So of course there's always more bureaucracy on the front end than on the back end of that. So I strongly advise involving the genetics team for these kinds of stat tests because we can certainly help grease the wheels. So that's karyotype.
Dr. Angela Scheuerle:
FISH is also useful for... It is useful, and it has its uses in the right place. It's useful for investigations of mosaicism. If you've got to count a large number of cells for something weird, FISH can be helpful. It's useful for secondary confirmation of translocations, particularly looking at parents to see if there's a balanced translocation. And it's useful for some of the contiguous gene syndromes, particularly Williams syndrome.
Dr. Angela Scheuerle:
Now I know I said before that FISH won't pick up translocations, and it won't as a first pass. However, it's very helpful when the lab's trying to find where something is and they can do a FISH with a specialized probe and compare it against the banded chromosomes and figure out that, oh, this little piece of chromosome 11 is actually stuck on the bottom of chromosome 2, even if you can't actually see it by just looking at the karyotype. So that's FISH and karyotype.
Dr. Angela Scheuerle:
The other test is a microarray. And they're important things to know about this test right up-front. The first thing is that it's not a “better” karyotype. It's a different test. It's the difference between a CBC and a blood culture. One doesn't replace the other and they both give you information, but they give you different kinds of information. Now having said that, it can be redundant to send both a chromosomes and a microarray. So it's always good to know which test is going to answer the question that you have.
Dr. Angela Scheuerle:
And it's always redundant, by the way, to send FISH and a microarray. A microarray is like doing FISH at hundreds of thousands of loci. These days, microarrays hit between 600 and 800,000 loci depending on the lab. So doing a separate targeted FISH test is really unnecessary. Lastly, a chromosome microarray is never the test to do if you're worried about a single gene condition like Noonan or achondroplasia. It's not that detailed. I tell families that the chromosome microarray is a mailman test, that looking at the chromosomes through a microscope, doing a routine karyotype, is like looking at the city from an airplane. You can see the big stuff, but I can't tell you if my mailman's come. The microarray is like knowing what mailboxes have mail in them. And then to go forward with the analogy, doing single gene testing is like looking at a bunch of envelopes. So microarray is the best test for things like 22q11 deletion because you can't always see it through a microscope. And it is for a number of other conditions at that level, but it's not good for details about single genes.
Dr. Angela Scheuerle:
Chromosome microarray is also not useful if you're worried about a balanced translocation. It absolutely will not see that. A microarray is looking at dosage and with a balanced translocation, the dosage is correct. So there's nothing for the microarray to see. They're also not the best test for mosaicism. Having said that, good, careful labs will report that the microarray suggests the mosaicism, but it will recommend doing a routine karyotype. So for example, if there's a baby with Turner syndrome, and this is something we need to do going forward, is so we have a baby who looks like there's Turner syndrome. And we need to know if there are any XY cells in that baby’s system because that changes the management. A karyotype is the best test because it will first confirm the diagnosis, but it will also evaluate for the mosaicism. A microarray may not find the XY cells or they may be present in low enough number that it doesn't rise above the level of artifact. So those are the three things, the karyotype, the FISH test, and the microarray.
Dr. Neeta Goli:
What is the typical turnaround time for each test?
Dr. Angela Scheuerle:
Interphase FISH, which doesn't require waiting for cells to multiply, as I mentioned can technically be done in a couple of hours. Right now, the UT Southwestern Veripath lab can turn it around in 24 hours. Routine FISH takes from three to seven days. Routine karyotype takes about a week, about seven days. A microarray with a routine result takes 10 days to two weeks and realistically, you got to remember that for all of these tests, the turnaround time can be longer if the cells don't grow or the sample's bad or there's a complex answer that needs further investigation. And if the sample needs to be shipped to a lab out of the city, that's going to add transit time.
Dr. Neeta Goli:
And since you mentioned cost earlier, how much do each of these tests cost?
Dr. Angela Scheuerle:
Oh, that's a broad question. That's so dependent on the patient's insurance and on the individual lab. I can give you very general numbers. A karyotype tends to run in the high $100s. Microarray tends to run in the low $1000s, somewhere between $1,000 and $1,200. FISH, that's going to depend on the lab. I know that the local lab FISH is something like $450 or $500, but that's regardless of the number of probes. It's the same cost regardless of how many probes to do, but it's really going to vary by lab.
Dr. Angela Scheuerle:
I would remind people that, and I say this all the time, that genetic testing is like space flight. You can have it good, cheap, or fast, pick any two. So if you want it fast and you want it cheap, you have to sort of question the lab. If you want it fast and you want it good, it's not going to be cheap. So that's sort of how I think about it. In general, geneticists have a set of labs that we're comfortable with because they have history and they know what they're doing and they're run by people who we trust. So that's how we tend to approach stuff, recognizing that everybody's insurance is also different.
Dr. Neeta Goli:
And then while we are waiting for the results of any tests to come back, how do you usually approach counseling these families?
Dr. Angela Scheuerle:
Well, I'm frequently asked about “will we have to wait for the test to give a diagnosis?” Well, you don't. My argument is that you don't need the test results to make a formal diagnosis. You absolutely should trust your instincts and your diagnostic abilities. Please call a genetics consult for input and support if we can help, but the team can all have the same approach so the parents are getting a consistent message. But if the baby clinically has Down syndrome, you talk to the family about Down syndrome. You talk about the test that's determining what type, but not that it's going to make or break the diagnosis. It works the same with the more complex cases. If the baby has multiple congenital anomalies, it's a baby who's affected by something. Might be chromosomal, might not be, but that's what you talk about. You talk about the multiple anomalies.
Dr. Angela Scheuerle:
And in general, I'm a believer in Osler’s statement that you get 85% of your information about caring for the patient from the history and physical. The lab should largely confirm what you've already identified. This means you don't need the lab result to make a formal diagnosis, or to put it in another way, you can go ahead and talk about the poor prognosis for a baby with holoprosencephaly and a heart defect, without needing to know that the diagnosis is chromosomal.
Dr. Neeta Goli:
And then to end today's episode, do you have any other advice for our listeners while they take care of newborns?
Dr. Angela Scheuerle:
I would ask people to remember that genetics isn't a subspecialty of pediatrics. It's an entirely separate medical specialty, and even the stuff that looks really simple can get complex very quickly. So take advantage of the fact that you have us available. We can help with all the things we've talked about. We can help plan and facilitate testing, and we can talk to the family about a likely diagnosis. And as I've been known to say, a genetics consult is going to be your least expensive genetic test.
Dr. Neeta Goli:
All right. Thanks so much for joining us today, Dr. Scheuerle.
Dr. Angela Scheuerle:
You're very welcome. Thank you for the opportunity to talk about all of this.
Dr. Neeta Goli:
Thanks for listening to Newborn News. We hope you join us next time. If you like what you hear, make sure to subscribe and leave us a review. If you have questions, comments, feedback, or suggestions for future episodes, please email me at NewbornNews@utsouthwestern.edu. As a reminder, this content is educational and is not meant to be used as medical advice. Views or opinions expressed in this podcast are those of myself and my guests, and do not necessarily reflect the views of the university.