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CML Testing Overview (Updated 2014)

CML leukemia testing CML testing overview CML tests explained CML terms explained CML terminology

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#1 Trey


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Posted 15 November 2014 - 12:03 PM

This is designed as a general overview to provide a basic layman's understanding of CML leukemia testing. It also explains some of the terminology which CML patients need to understand. I will avoid the jargon and keep this somewhat short, so this will not cover everything in detail. Always discuss your testing requirements with your doctor/Oncologist.


There are tests to diagnose CML, evaluate response to TKI drug therapy, assess the levels of the disease, and to check for specific problems. Among the terms used are Complete Blood Count (CBC), Bone Marrow Biopsy (BMB), Bone Marrow Aspiration (BMA), Cytogenetics Testing, Fluorescence In Situ Hybridization (FISH) testing, Polymerase Chain Reaction (PCR) testing, Comprehensive Metabolic Panel (CMP) testing, Kinase Domain Mutation testing, Gleevec Blood Level testing, and miscellaneous other tests.

When a person is suspected of having CML, testing is done to confirm the diagnosis. A Complete Blood Count (CBC) test will usually show a very high white blood cell (WBC) count, and may also show high platelets (PLT) and other abnormalities. But this does not confirm that a person has CML. The confirmation of CML is usually done by Cytogenetics Testing (cell testing) on white blood cells taken during a Bone Marrow Biopsy (BMB) process. During a BMB, a core sample is taken from the hip bone using a hollow needle, and marrow cells are collected that cling to that bone sample. During the same procedure, fluid from the hip marrow is also taken out by a syringe, and this second part is called a Bone Marrow Aspiration (BMA). So the BMA aspirate or fluid is extracted through the hole created during the BMB. Cytogenetics Testing is done on the core sample and aspirate fluid, whereby approximately 20 marrow cells are thoroughly examined by microscope in the lab for abnormalities, including the leukemic Philadelphia Chromosome (Ph+ chromosome), which is the indicator of CML, and a diagnosis can be made. The sample is also checked for other abnormalities, including secondary chromosome mutations, high blast count (immature WBCs), and other abnormalities such as marrow fibrosis, abnormal cell morphology (shapes and sizes), etc. So a BMB at diagnosis is critical to ensure a proper diagnosis. The aspirate fluid may also be tested by FISH and/or PCR testing to determine the relative amount of leukemic cells in the body (see later explanations). A follow-up BMB might be done again at six months post-diagnosis, and as needed after that if other tests show a suspected problem such as loss of response to drug therapy. When therapy reduces the levels of CML disease to where the Cytogenetics Testing (BMB or FISH) can no longer detect any Ph+ chromosome cells, that person has achieved a Complete Cytogenetic Response (CCyR) and BMBs are no longer necessary after CCyR unless a loss of drug response occurs.


After diagnosis, it is important to continually monitor response to therapy with regular tests. The most basic of these tests is the Complete Blood Count test, which assesses overall blood health. When a CBC test shows that blood counts have returned to normal levels, and especially the WBC and platelet counts, the person has achieved a Complete Hematological Response (CHR). After that, the CBCs should still be continued, but the frequency is often reduced. CML patients can often have certain blood counts become too low, especially white and red blood cell levels and platelet levels, so continued CBC monitoring is important during early treatment. Also, a rapidly rising WBC count could indicate the need for more testing and possibly a change in drug therapy, since it might indicate a loss of drug response.


The BMA marrow fluid taken during the BMB process can also be used to perform a FISH or PCR test. (FISH is fluorescence in situ hybridization and PCR is polymerase chain reaction). Or circulating (peripheral) blood can also be used to perform a FISH or PCR. Both FISH and PCR show the levels of CML disease, and are used to monitor progress, or detect setbacks or loss of response to therapy. A FISH test checks approximately 200 - 500 WBC cells, and counts the number of cells that have the Ph+ chromosome (technically it looks for the BCR-ABL gene in the WBC cells, which resides on the Ph+ chromosome). FISH is done by a machine which uses a dye process, isolates approx 200 - 500 cells, and counts the leukemic WBC cells. The result is given as a percentage of leukemic cells to good cells, so the person can say that X% of their WBC cells are leukemic. The limitation of FISH is that it can only count a small sample of cells, so if the level of disease is only a few percent, the FISH report will likely be zero (a zero FISH is also CCyR response, same as a zero BMB Test). So FISH is only used until CCyR is achieved. After CCyR only PCR testing can detect the remaining levels of Minimal Residual Disease (MRD), since PCR is far more sensitive than FISH. A trend among Oncologists is to start doing PCRs early instead of FISH, including at diagnosis, since PCRs can be used to track logrithmic (log) reductions in disease levels, and FISH cannot track log reductions (discussed later).  But it is usually wise to have FISH done until CCyR is achieved, since PCR is actually less accurate than FISH at higher levels of disease burden.  A zero FISH is roughly equivalent to a 2 log reduction as measured by PCR, or a 1% PCR using International Standard (IS) reporting.


There are two types of PCR tests. One is called a Qualitative PCR, which is a simple "yes/no" test that says it either detected BCR-ABL (leukemic cells) or did not detect them, but no number is provided - this is generally only useful to help diagnose CML since it helps distinguish between CML and other types of leukemia. The other type of PCR, the Quantitative PCR, counts the number of BCR-ABL (Ph+ chromosome cells) and reports it as either a ratio or as a percentage number, so this is the type of PCR that is useful to track treatment progress, especially in Minimal Residual Disease (MRD) status where the levels of Ph+ chromosome cells are low and harder to detect. Some Oncologists will do a baseline Quantitative PCR at or near diagnosis to establish a baseline from which to evaluate progress, especially toward a 3 log reduction in disease levels (the MMR goal).

PCR tests a sample of blood or marrow fluid, and can detect approximately 1 leukemic cell out of 100,000 or possibly 1 million cells in the sample, so the test is very useful for long term monitoring of disease levels and showing treatment progress. PCR testing can be done using either blood or BMA fluid. During a PCR test, the BCR-ABL in leukemic cells is counted and the result of the test is given as a percentage ratio of BCR-ABL (leukemic cells) to another gene in the cells (called a control gene). So PCR results are not a ratio of leukemic cells to good cells as we might think, which technically means that a PCR result is not actually a total percentage of leukemic cells in the body. This is one reason why PCR results from one person to another, and one lab to another, are not equivalent, due to lack of standardisation among labs regarding equipment and which control genes are used (there are several different control genes used for CML PCRs). That is a reason for sticking with the same lab, so the results will be directly comparable for each PCR done, and trends can be watched. It is important when switching labs that the first PCR from the new lab be used to set a new baseline, since it may not directly compare to the previous PCRs from the other lab. Most labs have now implemented International Standard (IS) PCR reporting in an attempt to standardise the test results among labs, which has both benefits and drawbacks.


PCR results are very useful for showing trends, whether progress or retrogression. The hope for PCR results is to see progress toward a 3 logarithmic (3 log) reduction from the level of disease that existed at the time of diagnosis. This 3 log reduction is called a Major Molecular Response (MMR). Your lab should provide the log number to usefor tracking log reduction progress, ask your Onc to provide it. The International Scale conversion attempts to standardise PCR results by using 100% as the pre-determined diagnosis starting point and .1% as a 3 log reduction which shows MMR, which is the major goal for CML drug therapy treatment.


PCR test results are not exact, and variations from one test to the next often occur, resulting in a roller-coaster of PCR numbers.  Here is the caution that Mayo Clinic puts on the interpretation of PCRs:

"The precision of this assay at low bcr/abl levels is relatively poor, such that inter-run variation can be as high as 0.5 log. Only level changes >0.5 log should be considered clinically significant. For example, if a result is given as 0.1% bcr/abl:abl, then any result between 0.05% and 0.5% should be considered essentially equivalent. If the results are being used to make major therapeutic decisions, significant changes during monitoring should be verified with a subsequent specimen."  Also, PCRs are not very accurate at high levels of leukemia.  Again, the emphasis is on trends in PCR reports, not on individual reports, which can fluctuate for many reasons unrelated to the patient's status (age of sample, lab processes, lab errors, etc).


If a 3 log reduction is achieved, the next goal becomes maintaining the 3 log reduction or even continued reduction toward a negative/undetectable PCR (PCR Undetectable or PCRU). PCRU is the point where the PCR is not sensitive enough to detect any leukemic cells in the sample. This PCRU is also called Complete Molecular Response (CMR), which is the deepest level of response currently measurable. In PCRU status, the leukemic cells are most likely still there, although fewer than 1 in a million. But research indicates there would likely still remain over 1 million leukemic cells in the body at the point of initial PCRU. This initial PCRU is roughly equivalent to a -4.5 log reduction in leukemic cells, depending on the lab. The patient can continue to drive down the number of leukemic cells after the initial PCRU is attained, but current monitoring techniques cannot assess the progress. There is no test to determine if a person with CML is actually cured (i.e., free of all leukemic cells). But continuous PCRU can be loosely called a "functional cure". Normally, the goal of CML drug therapy is to drive the number of leukemic cells to the lowest level possible, with the combined effect of stopping the advance of the disease, putting the CML patient into permanent, low level chronic phase CML.


Note that FISH percentages do not relate to PCR percentage numbers. For instance, at diagnosis I had both a FISH and PCR done. The FISH was 100% and the PCR was 8%.  It is not true that a low FISH means a low PCR. A FISH is like measuring the weight of something with your hand, and a PCR is like measuring with a surgical scale. Also, the FISH has an error rate of approx 1 - 5%, so your FISH could read 5% with older equipment but actually be zero. When the FISH result gets below approx 5%, you should rely on PCRs from then on. A recent trend is to perform PCRs from the start, but as discussed above, PCRs are actually not very accurate at high levels of leukemia.


If any of the tests, such as CBC, Cytogenetics, FISH or PCR, show the patient may be losing response to drug therapy, additional tests may be ordered. A Kinase Domain Mutation Test is one test that may sometimes show whether a certain TKI drug can no longer work. The results will show if a mutation in the BCR-ABL has occurred that prevents the drug from working, and an alternate drug can usually be used. Sprycel and Tasigna work against most mutations, but both do not work equally well against certain mutations, so this test can also help with alternative drug selection. (Just an added note on the word mutation, a kinase domain mutation is not the same as a secondary chromosome mutation such as Trisomy 8, Monosomy 7, etc). Below is one lab's description of this test:


Another CML related test is the Gleevec Blood Level Test, although this test has been discontinued by many labs. This test can show how much Gleevec is being absorbed into the bloodstream, since we all absorb and process drugs at different rates. So this test can show whether a person needs to take a higher dosage of Gleevec to ensure adequate levels of drug in the bloodstream.



There are other tests that are used for monitoring CML patients. A Comprehensive Metabolic Panel (CMP) test should be performed regularly (probably at the same time PCR is done). This checks a range of issues such as liver function, kidney function, metabolite levels, etc.to monitor for negative side effects:


Sometimes a Flow Cytometry test is used at diagnosis or when a problem is suspected.  This test counts numbers of cells by various types, and provides a picture of the cellular makeup of the blood or marrow.



Examples of some other relevant tests: CAT Scans or physical checks for enlarged spleen (left side pain), physical checks for enlarged lymph nodes, complete or partial physical exams. There are also other tests to check for other specific problems when suspected, such as thyroid function, iron levels, heart issues, colonoscopy, bone density, skin problems, etc.


A sample CML testing schedule might look like the following (assuming no complications) -- your Onc should determine your specific schedule:
Diagnosis: BMB/BMA, FISH and/or PCR; CMP; abdominal (spleen) CAT scan; physical
Weekly during first several months: CBC each week until WBC is normal
3 months: FISH and/or PCR; CMP
CBC now every 2 weeks
6 months: BMB/BMA; FISH and/or PCR; CMP
CBC now every 2 - 4 weeks
9 months: PCR; CMP
12 months: BMB/BMA (unless FISH/PCR already show CCyR), PCR; CMP
After 1 year: PCR and CMP every 3 months, CBC every 4 - 6 weeks; BMB only for loss of drug response

After 3 log response or PCRU: Possibly longer intervals - consult your Onc, but PCR, CBC, and CMP monitoring is still required at "regular" intervals

Your Onc should be following the National Comprehensive Cancer Network Guidelines for CML monitoring and treatment:


Other thoughts:

1) Get copies of every lab report - you will need them for reference. Also, your Onc will not normally take time to cover every issue with you during your office visit. Read all of your lab reports thoroughly. You must be your own health care advocate.

2) Only have specimen's drawn for PCR on Monday - Thursday.  Avoid Friday, or it may not be processed until Monday.  PCRs must be done as soon as possible on the specimen to have the most accurate PCR report.  By 48 hours the BCR-ABL has degraded by 50%, so your PCR would be very inaccurate (reports PCR result as lower than it actually is).

3) The color of the stopper on the specimen tube the blood or marrow fluid is drawn into: Green top is for BMB and FISH. Lavender top is PCR. See the link below, page two (all labs use the same color coding) Make sure your lab tech uses the correct color tube:

4) Here are some additional links:



BMB article:

CBC overview:

Comprehensive Metabolic Panel (CMP) test info:.

If testing reveals potential loss of response to drug therapy, you may want to discuss the following with your Onc:

If a PCR test suddenly shows a sharp increase (greater than 1 log - one decimal place) AND loss of CCyR:
1) Reaccomplish the PCR right away to assure it is accurate (sometimes things go wrong, such as degradation of the sample during shipping, contamination, lab errors, etc).
2) If the PCR result is confirmed, or at the same time as the PCR if you wish, have both a Bone Marrow Biopsy and a Kinase Domain Mutation test done. The latter tests for drug resistance, which is a primary cause of lack of response

3) Depending on what the drug resistance test shows, possibly increase Gleevec dosage if not resistant (but possibly assess Gleevec levels in the blood with a Gleevec Blood Level Test), or switch to another drug if you are Gleevec resistant.

Here is some info on Gleevec resistance:

4) Kinase Domain mutations are not the only reason for drug resistence.  Researchers have found that an over-expression of the LYN Kinase can also cause drug resistence:


5) If in the meantime you wanted to increase Gleevec dosage, I would discuss that with your Onc. If the PCR increases by 1 or 2 logs, it likely would mean Gleevec has stopped working and a drug change would be required. But an interim increase in dosage is still an option.

6) Leading CML specialists are recommending faster switching to Sprycel or Tasigna when loss of response to Gleevec starts to occur.

Edited by Trey, 16 November 2014 - 09:53 AM.

#2 alexamay09


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Posted 16 November 2014 - 05:56 AM

Excellent and useful information Thanks.

#3 missjoy


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Posted 20 January 2015 - 12:22 PM

Hi Trey

"A kinase domain mutation is not the same as a secondary chromosome mutation such as Trisomy 8, Monosomy 7, etc)."

what's a secondary chromosome mutation?
Is TkI effective for CML patients diagnosed with secomdary chromosome mutation?

#4 Trey


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Posted 20 January 2015 - 05:52 PM

A secondary chromosome mutation is one in addition to the main CML chromosome mutation, which is the Philadelphia Chromosome (9/22 translocation).  See this:




The most often seen secondary chromosome mutations are trisomy 8 and monosomy 7.  They are usually found by Bone Marrow Biopsy, or possibly FISH testing, so if the Onc has not said anything about them, there probably are none.  The CML TKI drugs usually resolve these over time.  But oddly, the drugs can also cause the secondary mutations.  Most Oncologists do not see these as a significant issue.  But they should be monitored if they exist.

#5 scuba


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Posted 29 March 2016 - 11:48 AM

Is there a way to make this a "sticky" ?

Diagnosed 11 May 2011 (100% FiSH, 155% PCR)

with b2a2 BCR-ABL fusion transcript coding for the 210kDa BCR-ABL protein


Sprycel: 20 mg per day - taken at lights out with Quercetin and/or Magnesium Taurate

6-8 grams Curcumin C3 complex.


2015 PCR: < 0.01% (M.D. Anderson scale)

2016 PCR: < 0.01% (M.D. Anderson scale) 

March        2017 PCR:     0.01% (M.D. Anderson scale)

June          2017 PCR:     "undetected"

September 2017 PCR:     "undetected"

#6 Buzzm1


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Posted 29 March 2016 - 12:32 PM

Is there a way to make this a "sticky" ?

The administrator of this forum can create a sticky, however, being that the remaining life of this forum could be short, they might be hesitant to do so.  If a sticky is created I would recommend it be in the form of a developing linked index so that it can continually be added to.  

For the benefit of yourself and others please add your CML history into your Signature


02/2010 Gleevec 400mg

2011 Two weakly positives, PCRU, weakly positive


2013 PCRU, PCRU, PCRU, weakly positive

2014 PCRU, PCRU, PCRU, PCRU (12/07 began dose reduction w/each continuing PCRU)

2015 300, 250, 200, 150

2016 100, 50/100, 100, 10/17 TFR

2017 01/17 TFR, 04/18 TFR, 07/18 TFR 0.0012, 08/29 TFR 0.001, 10/17 TFR 0.000

2018 01/16 TFR 0.0004 ... next quarterly PCR 04/17


At the earliest opportunity, and whenever possible, lower your TKI dosage; TKIs are toxic drugs and the less we take longterm the better off we are going to be ... this is especially true for older adults.  


In hindsight I should have started my dosage reduction two years earlier; it might have helped minimize some of the longterm cumulative toxic effects of TKIs that I am beset with.  


longterm side-effects Peripheral Artery Disease - legs (it's a bitch); continuing shoulder problems, right elbow inflammation.   GFR and creatinine vastly improved after stopping Gleevec.


Cumulative Gleevec dosage estimated at 830 grams


Taking Gleevec 400mg an hour after my largest meal of the day helped eliminate the nausea that Gleevec is notorious for.  


Trey's CML BlogStopping - The OddsStop Studies - Discussion Forum Cessation Study

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