ONCAlert | Upfront Therapy for mRCC

Case 1: Allelic Burden in FLT3+ AML

Targeted Oncology
Published Online:12:34 PM, Wed June 19, 2019


EXPERT PERSPECTIVE VIRTUAL TUMOR BOARD

Naval G. Daver, MD: This is a common case that a lot of us will see here: a newly diagnosed FLT3 ITD [internal tandem duplication]-mutated acute myeloid leukemia [AML]. It has some other mutations as well—TP53, ASXL1, RUNX1. Basically she’s coming to us here for evaluation.

Dr Weinberg, I’m sure you receive a lot of cases of this nature. What would be the triage and work flow in the hematopathology and molecular [laboratory tests]?

Olga K. Weinberg, MD: Every bone marrow, especially for patients with acute myeloid leukemia, would get a morphological evaluation—the aspirate smear. We’ll look at the appearance of the blast, we’ll look at the background cells, and we’ll look for dysplasia. We’ll tabulate all those findings, and at the same time we perform cytogenetic analysisnext-generation sequencing [NGS] analysis, sometimes an AML FISH [fluorescence in situ hybridization] panel. When all these tests come back, we can give a full WHO [World Health Organization] classification, which takes into account a presence of some of these cytogenetic abnormalities and mutations, and we show final diagnosis.

Before the cytogenetic tests come back, we can say it’s an acute myeloid leukemia. Of course, pending NPM1 mutation, we would say it’s just AML with NPM1, and it becomes NPM1-mutated AML. That’s how we work up acute myeloid leukemia.

Naval G. Daver, MD: What’s the timeline from when you get the aspirate biopsy sample to issuing an initial diagnosis? Then, in your group in Brigham [and Women’s Hospital], what are the main molecular findings that they’re looking for, and how quickly are those molecular and cytogenetic analyses becoming available?

Olga K. Weinberg, MD: We can look at an aspirate within a few hours of its being done, and flow cytometry, of course, is being done at the same time. Within a few hours, we can issue a diagnosis of acute myeloid leukemia. The next-generation sequencing, which at Brigham is called Rapid Heme Panel, comes back within a week, sometimes about 4 to 5 days, because we have a few runs a week. We should have a full diagnosis within a week. Cytogenetic analysis, we can have a read within 24 to 48 hours.

Naval G. Daver, MD: OK. Is it a practice that you’re seeing that physicians are waiting for this information, or are they proceeding with treatment and then using the molecular [test results] as the treatment is going on?

Olga K. Weinberg, MD: Well, it depends. If it’s an acute promyelocytic leukemia, some form of therapy will be started. Most of the time our clinicians will wait until next-generation sequencing is back, because that would really determine which trials patients go on. The results of that test are very crucial.

Naval G. Daver, MD: Yes. Anything different we’re seeing, Drs Rizzieri or Gergis, in your practice about molecular?

David Alan Rizzieri, MD: I think you’re in a very privileged site. The turnaround you’re provided as clinicians is pretty good for NGS. In most of our sites, that takes a couple of weeks, not to run the test, but because of all the data crunching that’s required. While we run the NGS panels, we do a separate PCR [polymerase chain reaction] for the targetable upfront lesions, probably what a number of the other clinical sites do. We would search for IDH mutations as well as FLT3 with separate orderables for PCR to get that turnaround within the first couple of days. Similar to what was mentioned, FLT3 obviously impacts our upfront therapy, and with recent approvals, so would the IDH, at least on-label. We would look for the same things, but have to get to it a little bit differently to try to get the results in a rapid fashion.

Naval G. Daver, MD: I think we do something a little bit similar, where we do an 8-gene molecular panel, which is a kind of a rapid panel that includes FLT3, IDH1/2, NPM1, TP53, and then RUNX1—so the most important—and then you get the larger panel. We get it in about 9 or 10 days, but that’s usually not something we’re waiting for in practice. I think looking for secondary, or MRC [myelodysplasia-related changes]-associated features, at least for FLT3, as well as cytogenetics, is important, and this actually impacts our standard of care. What about you, Dr Gergis?

Usama Gergis, MD, MBA: Similarly, we have our in-house panel that turns out FLT3 rather quickly, NPM1, and then we wait for the rest, and it takes about 4 to 7 days.

Naval G. Daver, MD: OK. What about IDH? Do you try to get the IDH before treatment, or are you really using it more for salvage decision?

Usama Gergis, MD, MBA: Depending on the clinical trials that we have—currently we do not have IDH upfront—we’ll depend on it in the salvage setting, or with a clinical trial or standard of care.

David Alan Rizzieri, MD: I’m interested in your sense, and maybe James’s and Olga’s, of the pathology here. With this presentation with a high white count and a FLT3, it’s always unclear to me how I interpret the allelic burden. In all of these other genetic changes, do we think of that as the driving problem, particularly with this high white count? I don’t typically think of FLT3 driver leukemias as presenting with such a high white count, necessarily. Maybe that’s just my misperception.

Olga K. Weinberg, MD: Well, NPM1-mutated AML does tend to present with a very high white count, so in that sense, it’s pretty typical. FLT3 by itself can also present with high white count. It’s not necessarily unusual. Of course, it probably also depends on how long before the patient was seen.

Naval G. Daver, MD: Yes. We commonly see the FLT3-mutated patients presenting with high white counts. I think your question is a very good one. How does the allele burden relate to the white count? We have not seen a clear correlation that those who are more highly burdened will come with more leukocytosis, or vice versa. Especially with the data that Dr McCloskey is going to talk about, we don’t even know therapeutically if it has an impact. We get the allelic burden, but I think a lot of sites don’t even get it. They just say positive or negative, but we don’t really do much on it. What do you do, James?

James K. McCloskey II, MD: I think that’s exactly true, and I think that where we find ourselves right now is in a position where we often have more information than we sometimes know what to do with. I think we haven’t yet standardized FLT3 testing well enough to know where that allelic burden cutoff should be for high or low. Even if you look at the different guidelines, they often set that cutoff at different places. The different trials have used different cutoffs for allelic burden. It’s certainly one of the challenges we face, not only in this example in an upfront setting, but also later and in the context of relapse. How do we determine which driver mutation is really the most important to target?

Olga K. Weinberg, MD: I would also add that variant allele frequency is very dependent on the kind of testing that you use, and it may not even be reproducible from one NGS panel to another. We recently reported on variant allele frequency in NPM1 mutation, which is generally a favorable mutation. Within those patients, it actually seems to subdivide into patients who don’t do well, who have a high variant allele frequency. In our study, it did correlate with blast count, so I think there’s a lot that we’re still learning.

Naval G. Daver, MD: Even between [laboratory tests], you may not have the same variant allele, so that makes it even more complicated.

Olga K. Weinberg, MD: Right. That makes it even more complicated, and it’s hard to draw that conclusion, but it does underline the biology.

Naval G. Daver, MD: Yes, very interesting. Go ahead, James.

James K. McCloskey II, MD: One of the other things we’re finding, especially as we have, fortunately, new therapeutic options that are available to patients and some of these results become more valuable to us, is that sometimes even the quality of the aspirate itself is so variable. As we start thinking about MRD [minimal residual disease] and all the other molecular tests, if we have a sample that’s drawn after 12 other mL have been removed, most of that is really peripheral blood. How does that really translate? Especially in this era where we are making important treatment decisions, I think it’s a real challenge for us.

Naval G. Daver, MD: Yes. Go ahead.

Olga K. Weinberg, MD: That would influence the variance.

Usama Gergis, MD, MBA: So is it safe to say that allelic burden for FLT3 ITD has no bearing in treatment decisions today?

Naval G. Daver, MD: I would say yes. Based on the treatment we’re going to discuss, I think if you’re positive, you’re positive, and negative…. Should you transplant people who are NPM1-mutated, low FLT3 allele, which is an emerging research topic? Today I think we would probably treat them, transplant them, give them midostaurin, and then move ahead.

Transcript edited for clarity.


EXPERT PERSPECTIVE VIRTUAL TUMOR BOARD

Naval G. Daver, MD: This is a common case that a lot of us will see here: a newly diagnosed FLT3 ITD [internal tandem duplication]-mutated acute myeloid leukemia [AML]. It has some other mutations as well—TP53, ASXL1, RUNX1. Basically she’s coming to us here for evaluation.

Dr Weinberg, I’m sure you receive a lot of cases of this nature. What would be the triage and work flow in the hematopathology and molecular [laboratory tests]?

Olga K. Weinberg, MD: Every bone marrow, especially for patients with acute myeloid leukemia, would get a morphological evaluation—the aspirate smear. We’ll look at the appearance of the blast, we’ll look at the background cells, and we’ll look for dysplasia. We’ll tabulate all those findings, and at the same time we perform cytogenetic analysisnext-generation sequencing [NGS] analysis, sometimes an AML FISH [fluorescence in situ hybridization] panel. When all these tests come back, we can give a full WHO [World Health Organization] classification, which takes into account a presence of some of these cytogenetic abnormalities and mutations, and we show final diagnosis.

Before the cytogenetic tests come back, we can say it’s an acute myeloid leukemia. Of course, pending NPM1 mutation, we would say it’s just AML with NPM1, and it becomes NPM1-mutated AML. That’s how we work up acute myeloid leukemia.

Naval G. Daver, MD: What’s the timeline from when you get the aspirate biopsy sample to issuing an initial diagnosis? Then, in your group in Brigham [and Women’s Hospital], what are the main molecular findings that they’re looking for, and how quickly are those molecular and cytogenetic analyses becoming available?

Olga K. Weinberg, MD: We can look at an aspirate within a few hours of its being done, and flow cytometry, of course, is being done at the same time. Within a few hours, we can issue a diagnosis of acute myeloid leukemia. The next-generation sequencing, which at Brigham is called Rapid Heme Panel, comes back within a week, sometimes about 4 to 5 days, because we have a few runs a week. We should have a full diagnosis within a week. Cytogenetic analysis, we can have a read within 24 to 48 hours.

Naval G. Daver, MD: OK. Is it a practice that you’re seeing that physicians are waiting for this information, or are they proceeding with treatment and then using the molecular [test results] as the treatment is going on?

Olga K. Weinberg, MD: Well, it depends. If it’s an acute promyelocytic leukemia, some form of therapy will be started. Most of the time our clinicians will wait until next-generation sequencing is back, because that would really determine which trials patients go on. The results of that test are very crucial.

Naval G. Daver, MD: Yes. Anything different we’re seeing, Drs Rizzieri or Gergis, in your practice about molecular?

David Alan Rizzieri, MD: I think you’re in a very privileged site. The turnaround you’re provided as clinicians is pretty good for NGS. In most of our sites, that takes a couple of weeks, not to run the test, but because of all the data crunching that’s required. While we run the NGS panels, we do a separate PCR [polymerase chain reaction] for the targetable upfront lesions, probably what a number of the other clinical sites do. We would search for IDH mutations as well as FLT3 with separate orderables for PCR to get that turnaround within the first couple of days. Similar to what was mentioned, FLT3 obviously impacts our upfront therapy, and with recent approvals, so would the IDH, at least on-label. We would look for the same things, but have to get to it a little bit differently to try to get the results in a rapid fashion.

Naval G. Daver, MD: I think we do something a little bit similar, where we do an 8-gene molecular panel, which is a kind of a rapid panel that includes FLT3, IDH1/2, NPM1, TP53, and then RUNX1—so the most important—and then you get the larger panel. We get it in about 9 or 10 days, but that’s usually not something we’re waiting for in practice. I think looking for secondary, or MRC [myelodysplasia-related changes]-associated features, at least for FLT3, as well as cytogenetics, is important, and this actually impacts our standard of care. What about you, Dr Gergis?

Usama Gergis, MD, MBA: Similarly, we have our in-house panel that turns out FLT3 rather quickly, NPM1, and then we wait for the rest, and it takes about 4 to 7 days.

Naval G. Daver, MD: OK. What about IDH? Do you try to get the IDH before treatment, or are you really using it more for salvage decision?

Usama Gergis, MD, MBA: Depending on the clinical trials that we have—currently we do not have IDH upfront—we’ll depend on it in the salvage setting, or with a clinical trial or standard of care.

David Alan Rizzieri, MD: I’m interested in your sense, and maybe James’s and Olga’s, of the pathology here. With this presentation with a high white count and a FLT3, it’s always unclear to me how I interpret the allelic burden. In all of these other genetic changes, do we think of that as the driving problem, particularly with this high white count? I don’t typically think of FLT3 driver leukemias as presenting with such a high white count, necessarily. Maybe that’s just my misperception.

Olga K. Weinberg, MD: Well, NPM1-mutated AML does tend to present with a very high white count, so in that sense, it’s pretty typical. FLT3 by itself can also present with high white count. It’s not necessarily unusual. Of course, it probably also depends on how long before the patient was seen.

Naval G. Daver, MD: Yes. We commonly see the FLT3-mutated patients presenting with high white counts. I think your question is a very good one. How does the allele burden relate to the white count? We have not seen a clear correlation that those who are more highly burdened will come with more leukocytosis, or vice versa. Especially with the data that Dr McCloskey is going to talk about, we don’t even know therapeutically if it has an impact. We get the allelic burden, but I think a lot of sites don’t even get it. They just say positive or negative, but we don’t really do much on it. What do you do, James?

James K. McCloskey II, MD: I think that’s exactly true, and I think that where we find ourselves right now is in a position where we often have more information than we sometimes know what to do with. I think we haven’t yet standardized FLT3 testing well enough to know where that allelic burden cutoff should be for high or low. Even if you look at the different guidelines, they often set that cutoff at different places. The different trials have used different cutoffs for allelic burden. It’s certainly one of the challenges we face, not only in this example in an upfront setting, but also later and in the context of relapse. How do we determine which driver mutation is really the most important to target?

Olga K. Weinberg, MD: I would also add that variant allele frequency is very dependent on the kind of testing that you use, and it may not even be reproducible from one NGS panel to another. We recently reported on variant allele frequency in NPM1 mutation, which is generally a favorable mutation. Within those patients, it actually seems to subdivide into patients who don’t do well, who have a high variant allele frequency. In our study, it did correlate with blast count, so I think there’s a lot that we’re still learning.

Naval G. Daver, MD: Even between [laboratory tests], you may not have the same variant allele, so that makes it even more complicated.

Olga K. Weinberg, MD: Right. That makes it even more complicated, and it’s hard to draw that conclusion, but it does underline the biology.

Naval G. Daver, MD: Yes, very interesting. Go ahead, James.

James K. McCloskey II, MD: One of the other things we’re finding, especially as we have, fortunately, new therapeutic options that are available to patients and some of these results become more valuable to us, is that sometimes even the quality of the aspirate itself is so variable. As we start thinking about MRD [minimal residual disease] and all the other molecular tests, if we have a sample that’s drawn after 12 other mL have been removed, most of that is really peripheral blood. How does that really translate? Especially in this era where we are making important treatment decisions, I think it’s a real challenge for us.

Naval G. Daver, MD: Yes. Go ahead.

Olga K. Weinberg, MD: That would influence the variance.

Usama Gergis, MD, MBA: So is it safe to say that allelic burden for FLT3 ITD has no bearing in treatment decisions today?

Naval G. Daver, MD: I would say yes. Based on the treatment we’re going to discuss, I think if you’re positive, you’re positive, and negative…. Should you transplant people who are NPM1-mutated, low FLT3 allele, which is an emerging research topic? Today I think we would probably treat them, transplant them, give them midostaurin, and then move ahead.

Transcript edited for clarity.
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