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Interpreting qPCR results


Hi all,

My lab results at diagnosis were as follows:
"Quantitative PCR: bcr-abl1/abl1 (IS) = 40,98% with expression of control gene abl1 = 1 308 000"
FISH test showed translocation t(9;22) in 95% of cells. Started therapy with Imatinib.

Three months later:
qPCR = 24,17% with expression of control gene abl1 = 629 000
FISH showed a complex translocation t(7;9;22) present in 75% of cells.
Imatinib was declared as failure, started on Tasigna instead.

Four months later (now):
qPCR = 4,44% with abl1 = 624 000
FISH showed t(7;9;22) presence of 30% as well as trisomy 8 in 6% of cells.

Doctor (hematologist) pointed at expression of abl1 gene as being too high (624k), and that together with trisomy 8 it shows that Tasigna (and any other TKI) are ineffective, with bone marrow transplant being the only remaining option.

Whenever someone quotes qPCR tests they only mention the percentage. So I'm wondering what is the significance of control gene expression? What are high or low values for this number?


Bone marrow transplant is an absolute LAST resort. You are not there yet by a long way. As long as your blast cell count is low (i.e. < few percent, ideally zero), you have time on your side to try the different drugs.

Imatinib and Tasigna work similarly with Tasigna binding to the ATP site on bcr-abl more tightly. No surprise your response is not much better. You need a different drug (i.e. dasatnib) which attacks bcr-abl differently and at higher order cells.

Ask your doctor for you to be switched to dasatinib and track your response 4 weeks later. Dasatinib may very well work and drive your FISH levels down. Right now FISH is the most important measure of treatment success. PCR is not as important until after your FISH levels are zero so no need to be concerned about bcr-abl/abl ratio's.

You should start dasatinib no higher than 70 mg preferably 50 mg. Given your trisomy 8 (which I have), you are likely susceptible to myelosuppression. Dasatinib is potent. Start at 50 mg and go up if needed (I take 20 mg and I am "undetected"). Assuming you start dasatnib, you will need weekly CBC blood tests to track blood cell counts.

There are other drugs as well (ponatinib, bosutinib, etc.) and you should be tested for the T315i mutation as appropriate to rule that out.

The sooner you switch the better.

I’m sorry I don’t have time to write you a proper reply right now - but you may find some answers to your questions in our PCR Primer:


Blarn, since the complex variant translocation was not observed at diagnosis but was subsequently observed via cytogenetic testing at 3 and 7 months along with trisomy 8 (do you know if your trisomy 8 is in leukemic or nonleukemic cells?) at 7 months suggests clonal evolution has occurred.  This may place you in a higher risk category suggesting genetic instability. Albeit you have demonstrated response with imatinib/nilotinib with your FISH results dropping from 95% to 30% which is a good sign.  As Scuba mentioned, it may be worth trying dasatanib.  Many folks who have switched from Im or NIl to dasatanib have shown significantly improved response. This TKI operates by binding to an alternative site on the kinase as well as inhibits other signaling pathways like Src and Stat5.

Thank you all for replies. I didn't know that FISH results were the more important indicator at this stage. Was trying to understand why SCT would be a recommended option, reading about it was quite discouraging. One of doc's arguments was that doing it earlier increases chance of success.

Scuba was spot-on about myelosuppression, already having it on Tasigna (platelets dropped to 55 x10^9/L but bounced up to 75, with hemoglobin at 92 g/L), meaning it would not work out long-term.

The first google result on cml trisomy 8 is a study suggesting that it might not be a big deal:

Will look more into Sprycel and bring it up on next appointment.

Thanks again!

One of members, Lucas, had a Trimsomy 8 at one point (some years back). If you use the search function on this site and search for “Lucas trisomy” you’ll find his story. I heard from him the other day, and he’s doing absolutely brilliantly at the moment - a very low PCR. I think he is still on nilotinib, but not 100% sure.

Here’s one of his posts, but search for more:

PCR really comes into it’s own at the lower levels as it can detect extremely low amounts of CML - but it is not to say it’s not useful before that. The most useful test in the early days is FISH on bone marrow, but there’s only so often you want to do that! 


Hi, david! Hope you're fine!! well, i had the trisomy 8, but it were on PH negative cells (healthy cells). If the trisomy is on PH positive cells, than you have a problem. that's a clonal evolution, a sign of accelerated phase. I have a friend who  had trisomy 8, double PH, etc. etc., and other translocations and did well on dasatinib 140mg, and, than on dasatinib 180mg (his doctor is a worldwide cml specialist). he got to MMR and eventually had a pleural effusion, changed to tasigna and all is well. it was 5 years ago, and he's alive and kicking and MMR. Good luck!!