[Carol D.]

FISH results interpretation

by Carol D. on Wed Dec 17, 2014 7:48 pm

I was diagnosed in Feb 2013 and had ASCT in June 2013. I have been in remission since. My first FISH report has never been explained to me, my oncologist and transplant doctor weren't able to decipher it for me (disturbing, I know). At any rate, it has been troubling me that I don't really know what it means, so I thought I'd give it a stab here for interpretation. Here goes:

DNA FISH PROBE
Comments: multiple myeloma Panel LSI ATM (11q22.3) SG/p53(17p13.1) SO< LSI RB! (13q14), LSI FGFR3 (4p16) SO/IGH (14q32) SG dual color, dual fusion and LSI IgH (14q32) SG/MAF (16q23) SO dual color dual fusion, Abbott Molecular Inc.

SCREENED CELLS, 803
MOLGEN
IMAGED CELLS 5

FINAL RESULT
Comments: nuc ish (RB1X1) {39/250}/(FGFR3X4, IGHX3) {59/166}/(IGHX3,MAFX2) {71/203}

INTERPRETATION
Comments: Positive for the RB1 deletion of the long arm of chromosome 13 in 39 of 250 cells analyzed (15.6%). Positive for a gain of two copies of the FGFR3 locus on the short arm of chromosome 4 in 59 of 166 cells analyzed (35.5%). Positive for a gain of the IGH locus on the long arm of chromosome 14 in 130 of 369 cells analyzed (35.2%).

It goes on some more with comments that are equally as nonsensical to me. Is this enough information for someone to give me a sense of what my FISH results mean?

I am currently on Velcade maintenance once every 2 weeks. Any information would be greatly appreciated!

[Carol of Eden]

Re: FISH results interpretation

by Carol of Eden on Thu Dec 18, 2014 1:49 am

Hi Carol D,

Are you a Kaiser patient in Southern California? Your FISH test format reads verbatim the same as mine (results slightly different, but same probes run, exact same wording). I too found that my oncologist could not discuss it with me except to say I did not have high risk FISH results. I complained to the transplant doctor that they didn't run enough panels (nothing to determine abnormalities of chromosome 1, for instance) and he just waffled. But maybe I am too demanding.

I studied quite extensively to understand my test and I have some insights into your results and how to read them.

For instance, you have deletion 13, a VERY COMMON finding, which used to be considered bad, but now is just considered normal. Abbott Molecular is a primary provider of these FISH probes to labs, and you can look them up and see the list of FISH probes they offer and info as to what each test means. "LSI" is just part of the labeling - name of the particular test listed on your report - that they ran. I think it may stand for the company that Abbott bought out that originally made that test, but that is an aside.

So, when they show (near the top) the list of FISH probes they ran (each tests for specific abnormalities on specific chromosomes), where they list LSI RB1 (13q14), that is a probe to see how many copies you have of the gene "RB1" on section number 14 of the "q" arm on chromosome 13. Below that under "FINAL RESULT" they list "RB1x1", meaning that they found an abnormality (they are only showing what was abnormal under "FINAL RESULTS" ), which is that you have only ONE copy of RB1, not the normal 2 copies. The {39/240} means they found this in 39 out of 240 cells they tested, not all of them.

They mention this in the "INTERPRETATION" below. When they say "positive for the RB1 deletion of the long arm of chromosome 13", it's funny wording because, in this case, "positive" for a deletion means the same as being "negative" - i.e., missing - for one of the normal copies of the chromosome.

FRG3X4 means that they found 4 copies of the FRG3 gene, in your case with three copies of the IGH gene. In that probe which they listed above as "LSI FGFR3 (4p16) SO/IGH (14q32) SG dual color, dual fusion" (and you can find on the Abbott site), they are really looking for the 4:14 translocation, which is considered somewhat high risk. I'd like to see what else they said that you didn't quote - maybe it refers to this finding again.

In my case, they found 3 copies of FGFR3 but only 2 of IGH. They commented that it "may represent a rearrangement", which is another word for translocation. I have researched and found that sometimes when a translocation occurs, half of the IGH locus can disappear. I'm guessing your result is a bit ambiguous. I think if they saw direct evidence of a translocation they would have said so. In my case, they also said it could be an extra copy of chromosome 4 (perhaps you have TWO extra copies of chromosome 4). I saw a doctor on the Beacon forum comment to another patient that extra copies of 4 are not a bad indication at all.

The third result they mention, an extra copy of IGH when they probed for a 14:16 translocation (the last test on the list), says they do NOT see an extra signal for chromosome 16 (the MAF gene on that chromosome). I don't know how to interpret this, but if you study the probes on the Abbott site, you will see that the tests for translocations are designed so that if the chromosome splits for the translocation, they see two fluorescent dots of color instead of one larger dot (for the intact chromosome). And they can tell if a green and orange dot are right on top of each other (what they call a fusion - and why they call the test "dual color, dual fusion"), that the green (say it's the IGH) and the orange (MAF) have split and translocated to combine parts of each chromosome together. If they only see one dot, it could be that half the chromosome disappeared, or it could be that it is normal.

I'm sorry it is so confusing, and I hope I have not made your confusion worse! I felt like I was drowning when I tried to figure this out (it only seemed to hold critical clues to my life and death after all!), but slowly I understood more and then was just frustrated the doctor could not answer my questions!

[Carol D.]

Re: FISH results interpretation

by Carol D. on Thu Dec 18, 2014 3:36 pm

Thank you for your lengthy reply. Yes, I have Kaiser So Cal. The hematologist is in Irvine and transplant doctor in Sunset. Both doctors told me I have high risk myeloma but didn't explain why they thought so. The remaining comments are as follows:

COMMENT 16
Comments: F.I.S.H. with the LSI ATM (11q22.3) SG/p53 (17p13.1) SO,LSI RB1 (13q14), LSI FGFR3/IGH {t(4;14)}, and LSI IgH/MAF {t(14;16)} probes in the panel revealed ONE signal for the RB1 gene in 39 of 250 cells analyzed (15.6%), FOUR signals for the FGFR3 locus in 59 of 166 cells analyzed (35.5%), and THREE IGH/MAF probes in 59 of 166 cells analyzed (35.5%), respectively. The remaining probe sets showed the normal signal patterns for chromosomes 11q22.3 (ATMx2) and 17p13.1 (p53x2), and were negative for the FGFR3/IGH and IGH/MAF translocations. Please note, these findings are positive for the 13q14 (RB1) deletion on chromosome 13, the gain of two copies of the 4p16 (FGFR3) region of chromosome 4 or two chromosomes 4, and the gain of one chromosome 14 or the 14q32 (IGH) region of chromosome 14 which may represent an IGH rearrangement. These findings have been reported in cases of multiple myeloma with abnormalities involving chromosome 13 reported in 50% of cases. Refer also to 0441M-13.

Does that help explain more? I have a college degree, but obviously don't have an aptitude for chemistry and this makes no sense to me. If the doctors I'm seeing can't or won't explain it, I'm not sure why it's done except as protocol. Why would they both say I'm high risk based on this?

I'm pretty frustrated with the fact that Kaiser doesn't have a myeloma specialist and will likely pursue getting approval to see a myeloma specialist covered by them after the first of the year. Has anyone with Kaiser been successful with that pursuit?

I also read the posting on this site about my similar indicators of 4 and 14 not representing a translocation but gains which were a more positive side - just wondering what my high risk is, based on my doctor's assessments. All of my other indicators were not exceedingly high, just the percentage of plasma involvement as indicated by this FISH test. Comments?

[Dr. Adam Cohen]

Re: FISH results interpretation

by Dr. Adam Cohen on Thu Dec 18, 2014 11:25 pm

Dear Carol D,

Your FISH testing shows deletion of part of chromosome 13 (del13q) and extra copies of portions of chromosomes 4 and 14, without a (4;14) translocation. There is no deletion of 17p and no (14;16) translocation. So you do not have any high risk abnormalities by FISH.

It is worth asking your oncologist why he/she considers you to have "high-risk" disease. The important thing, however, is that you are 2.5 years out from transplant and still in good remission, so I certainly wouldn't change course at this point.

Hope this helps.

[Carol D.]

Re: FISH results interpretation

by Carol D. on Fri Dec 19, 2014 12:51 pm

Thank you so much Dr. Cohen for your reply! That is indeed good news! I'm actually one and a half years post transplant and continue to be in remission, although my most recent tests have some questionable oddities and will re-test in January.

Thank you again!

[Carol of Eden]

Re: FISH results interpretation

by Carol of Eden on Fri Dec 19, 2014 1:20 pm

Hi Carol,

Thanks for posting the rest of that report. If you do see a specialist and can discuss the report in detail.

I guess if it were me, my question would be "does the 3rd signal for IGH suggest the possibility of a translocation they did not test for?" It seems they tested for the 4:14 and 14:16 translocations, both of which would confer higher risk. I don't think they tested for the 11:14 translocation (although the first probe listed involves chromosome 11, I don't think it tests for 11:14) - but even if you had that, it is NOT a high-risk mutation. Much rarer are 14:20, 8:14 and (I think) 6:14. But you could have an extra 14 chromosome, or an extra part of the chromosome that includes the IGH locus.

I was dismayed to find that Kaiser does not have multiple myeloma specialists. I have not tried to get approval for an outside consultation, but have considered that or just paying out of pocket for one. I am smoldering since a year ago, and MGUS since 2009.

Since you had a stem cell transplant, I assume that was at City of Hope and I know they have a lot of expertise there. The transplant doctor I met with at Kaiser Sunset said that a panel reviews decisions in each case. Knowing that other doctors (presumably including an multiple myeloma specialist?) reviewed one's case (as well as others in the course of a meeting - ?) is not the same as meeting face-to-face with a specialist and being able to ask questions directly, and then follow-up questions. It does not let them get to know you as a real human being rather than a name with test results and clinical history.

What experience did you have with the doctors and facilities with your transplant process? Do you think you got the right treatment at the right time? Since they consider you to be high risk, are they offering you maintenance therapy?

[Carol D.]

Re: FISH results interpretation

by Carol D. on Fri Dec 19, 2014 1:55 pm

Yes, I was at City of Hope and received excellent care. I was hospitalized 19 days because, toward the end of my stay, I had a fever. Other than that, my transplant went very well. My doctor at COH was from the Sunset office. If I had to do it over again, I would request a different doctor because I find he is hard to understand because of his accent and he speaks very quickly. Many times I asked him to repeat information and to spell it. Other than that, the treatment was exceptional.

When I have asked my local hematologist about seeing a specialist, he says they consult one another on most of their cases, so they're an equivalent of a specialist. Yeah, right. At any rate, he did his residency under Dr. Vescio and told me if he deems it necessary, he would consult with him. As you say, that's not the same as me having a face to face conversation with him. I have considered going and paying outright for it but will probably wait until there is something out of line that requires making changes.

That being said, I do feel that I have received adequate care for my case to date. It is just disturbing that my doctor doesn't have the depth and breadth of knowledge of multiple myeloma. When I asked him about the Hevylite chain test because I am IgA lambda, he didn't know anything about it. He said he'd research it and we'd discuss it at my next appointment in February. He didn't go to ASH this year but said he thinks one of his colleagues was going, or at least was going to a summary meeting and would share with them.

It will remain to be seen at what point in time I deem it necessary to go outside of the Kaiser system to try to manage this. Hopefully it will be my good fortune to stay in remission for quite sometime and continue status quo for a while.

[Carol of Eden]

Re: FISH results interpretation

by Carol of Eden on Fri Dec 19, 2014 6:33 pm

Glad to hear about the excellent care you received. I was sent to meet with a transplant doctor, and was told I would be a candidate, if I progressed. It was Dr Cai, and I had that problem with understanding his accent. He was very pleased with the results of allo transplants from about 9 years ago, but I assume that was part of a trial. He said he thought I would need treatment in 1-2 years, and most likely due to infection. I was recovering from a 2-month respiratory tract infection, but have been somewhat better since. My functional Ig levels are pretty low (but I've seen worse).

I feel much as you about getting outside expertise. The obvious concerns are that signs of progression not be missed, delaying treatment and resulting in damage to bones / kidneys; and to get the RIGHT treatment. Although I can figure the cost of a consult (or ongoing consultation) - I was thinking of Dr. James Berenson - what if he says I need additional testing? Would Kaiser order the testing on his recommendation, or would I have to pay out of pocket (could be expense of another magnitude).

I feel I am being followed well in terms of lab tests. I am a bit concerned that it will be hard to get more advanced imaging than x-rays, and x-rays are slow to show bone damage. I've had a pain in one collar bone for 9 months, and mention it to my hematologist each time I see her. Maybe if it continues I will push for an MRI or PET scan.

I would like to have more FISH probes run, to find the extent (if any) of unidentified trisomies, and any chromosome 1 abnormalities (which are high-risk). I've seen a few FISH reports from Kaiser patients, such as yours, and they run the exact same probes for everyone. Once treatment begins and plasma cells are beaten back, the evidence is destroyed (until relapse), so down the road if they find that a particular drug works well or not for a certain cytogenetic type, I might not know enough about my disease history.

I realize we can't know everything about our cytogenetics, but more COULD be known before the chance is lost. SO - if a new BMB is contemplated - do I have to run out first and get an multiple myeloma specialist who can request some of the tissue to be transferred to an outside lab?

Anyway, I also think that any input as to treatment might not be useful at this point because by the time I (or you) need treatment, the options and knowledge base may have changed. My hematologist said she does not go to ASCO or ASH but to a "best of" session - probably what you alluded to. I try to gently push for things I want without rocking the boat, but that is just my nature. I hope like you to remain stable a long, long time.

[LarryD]

Re: FISH results interpretation

by LarryD on Sat Dec 20, 2014 5:06 pm

Carol D.,

Like you and Carol of Eden, my wife is a Kaiser SoCal patient and she had the same multiple myeloma FISH panel. It's very helpful that you posted your entire report, even though it may seem inscrutable.

There is one important thing that you did not mention: What was the percentage of plasma cells in the sample from your bone marrow biopsy? This is not in the FISH report, but instead is in the pathology report from the biopsy. This number is important as a measure of the extent of the disease, but it is also important for interpreting the FISH results.

As carried out at Kaiser's lab, each FISH probe involves examination of around 200 cells. These are random cells from the BM sample, and some of them are normal cells rather than cancer cells. Whereas plasma cells are only a few percent of the cells in the bone marrow of a healthy person, if the percentage of plasma cells is more than about 10%, it's a good bet that most of them are cancerous. If that percentage is very high, say 60% or more (as it often is when multiple myeloma is first diagnosed), then the FISH probe is seeing a lot of myeloma cells and it's likely to detect the anomalies for which it's looking if any are present. If the percentage is low, then only a few of the hundreds of cells examined are cancerous, and it's easily possible than an anomaly is actually present but not in those few cells, so it's not detected.

Your report says that a total of 805 cells were examined. If I break down your report, I find that there were 6 statements of positive findings:

1. Positive for the RB1 deletion of the long arm of chromosome 13 in 39 of 250 cells analyzed (15.6%).
2. Positive for a gain of two copies of the FGFR3 locus on the short arm of chromosome 4 in 59 of 166 cells analyzed (35.5%).
3. Positive for a gain of the IGH locus on the long arm of chromosome 14 in 130 of 369 cells analyzed (35.2%).
    
   F.I.S.H. with the LSI ATM (11q22.3) SG/p53 (17p13.1) SO,LSI RB1 (13q14), LSI FGFR3/IGH {t(4;14)}, and LSI IgH/MAF {t(14;16)} probes in the panel revealed:
    
4. ONE signal for the RB1 gene in 39 of 250 cells analyzed (15.6%),
5. FOUR signals for the FGFR3 locus in 59 of 166 cells analyzed (35.5%),
6. THREE IGH/MAF probes in 59 of 166 cells analyzed (35.5%), respectively.

1 and 4 are the same thing stated twice, as are 2 and 5. 3 and 6 also seem to be the same thing; the number of cells analyzed is different, but the percentage is essentially the same.

1,2,3 also correspond respectively to the information under "FINAL RESULT", but the 3rd result (gain of IGH on ch 14) has still a 3rd set of numbers (71/203). I don't understand these inconsistencies. Eliminating the duplicates gives a total of 785 "cells analyzed', slightly fewer than the 805 mentioned earlier. The anomalies were found in 15.6% to 35.5% of the cells, so it seems that you must have had at least 35.5% plasma cells in your BM sample.

You didn't mention when your bone marrow biopsy (BMB) was done. I'm assuming that it was at diagnosis. Have you had more than one?

It might be instructive to consider my wife's results, which are different. (Diagnosed September 2012, ASCT February 2013.) She has had 3 BMBs, each with FISH: first at diagnosis, then pre-transplant (Day -34), then post-transplant (Day +44). The fraction of plasma cells was 65%, 5%, and 3%, respectively. Anomalies found in each FISH analysis:

  del(17p) 16/29 (6.2%) 0/250 (0%) 7/24 (29.2%)
  t(4;14) 30/250 (12%) 0/250 (0%) 8/53 (15.1%)
  +11q13 18/259 (6.9%) 0/250 (0%) not tested
  del(13) not tested not tested 7/44 (15.9%)
  +15 not tested not tested 1/61 (1.6%)

The important things to notice are:

• In the first BMB, most cells were plasma cells, so the low percentage of cells with the anomalies shows that a low percentage of the *cancer* cells had those anomalies.
• In the 2nd BMB, no anomalies were detected, but the sample was diluted because 95% of the cells examined were normal ones. The same anomalies could have been present but were missed.
• The 3rd BMB was very different. It was done at City of Hope's lab rather than Kaiser's. They used "targeted FISH" (T-FISH), in which the sample is first purified to select out just the plasma cells and only those cells are examined. Thus, even though the number of cells examined per probe was smaller (24 to 61 rather than around 250), the test is far more sensitive. The harmful anomalies were found in an even higher fraction of cells than at diagnosis, but there were still fewer of these cells (I estimate 0.9% of all cells for del 17p) because there are fewer cancer cells altogether.

I hope this helps.

Best wishes,
Larry

[Carol D.]

Re: FISH results interpretation

by Carol D. on Sat Dec 20, 2014 7:36 pm

Thanks, Larry. The test posted was my first test done as part of diagnosing multiple myeloma. I've looked through all of my documents and don't find that I have that pathology report. This test was done early February 2013. The physician's assistant called me on the phone with the results and, when I asked her how bad it was, she said it was about 90% affected cells, but she's also the one who told me I had stage 4 and I told her that, as far as I'd read, there were only 3 stages. I haven't had a lot of confidence in them from the get-go, but I had multiple rib fractures at diagnosis and had been suffering with these for about 5 months, so I was exhausted and overwhelmed from the beginning.

My second BMB was pre-transplant in June and the results negative for translocations and that I was in remission. Dr. Cai said it was good because they only found 1% polytypic plasma cell population. He said the polytypic language was good.

It's all still Greek to me. I thought that was why they went to medical school.

Fortunately I have only had the two BMB's to date.

All of that being said, I am currently feeling pretty good and, although my IgG / IgA / IgM levels are all still below normal and my RBC's have never fully recovered, I'm feeling pretty good and satisfied with my bi-weekly Velcade maintenance.

It is noteworthy that I was the one who suggested Velcade bi-weekly as maintenance therapy to my doctor. I hadn't tolerated Revlimid from the onset and tried it unsuccessfully for maintenance, but it dropped my blood counts too much. He wasn't familiar with Velcade being used as maintenance (or it hadn't been sufficiently proven and studied), but after awhile he agreed it would be okay for me as opposed to no maintenance.

I know I need to be as informed as I can be about this disease, but it would be really nice to feel very confident that the doctor managing my case had a far superior knowledge of multiple myeloma specifically.