28 replies to this topic

[Sneezy12]

Happy Memorial Day to all of my fellow Veterans!

I have been Undetectable for 2 and 1/2 years.

My recent Test showed a "very low Quantitative level of less than 0.003% I.S., of Total ABL1".

I am not concerned about the value, but I noticed that it also said "The analytical Sensitivity of this assay has been determined at 0.003% (MR 4.5)".  

However, my previous Undetectable Tests all said "The Sensitivity has been determined at 0.01%".

I therefore assume that the Lab has increased the Sensitivity of the Test from 0.01% to 0.003%.

Am I correct?

Thank you, Frank

 

[cmljax]

Same thing happened at the lab (Mayo Clinic in Rochester) where my PCR is done.  A further question is before the sensitivity of the assay changed from .01% to .003%, was a result less than .01% considered undetectable? My latest test said less than .003% - is this undetectable or weakly detectable but not quantifiable?

 

I am getting really confused about what PCRU really is from a PCR result standpoint - maybe one of the braniacs like Trey or Scuba can clarify this for us.

[Sneezy12]

My Lab is Mayo also!

[Trey]

This indicates Mayo has changed the level to which they report BCR-ABL positivity.  It does not necessarily indicate they have changed their testing procedures, or that their test is now more sensitive.  But they have apparently decided to report positivity down to -4.5 log instead of -4.0 log.  Probably most labs report down to -4.5 log.

 

All PCR tests are capable of showing positivity down to at least -7 log, but studies have shown the false positives are too high below -5 log.  So labs will arbitrarily cut off the positivity reporting at some point, and the range is generally - 4 to -5 log.

 

So some people are PCRU because their lab does not report below -4 log.  This has not been a significant issue until recently, when TKI cessation has become an option.  Now test sensitivity going into cessation becomes more important.

[cmljax]

I know it is really just semantics, but is my last result was as follows:

 

Positive. BCR/ABL1 p210 mRNA transcripts were detected at a very low quantitative level (<0.003% of total ABL1 (%BCR/ABL1(p210):ABL1).

 

Is this same as PCRU or does the result have to actually say NEGATIVE for it to be officially considered PCRU?

[Trey]

It says "positive" so it was detected at some level.  You do not know if it was at -4.51 log or -7 log.  It is a bit disingenuous for Mayo to have a cut-off for reporting, but then still report the weak positivity. 

 

There is no standardized "official" PCRU since there are various cut-off limits.  But we treat it as below the lab cut-off limit since it really does not matter.

 

However, if someone is contemplating cessation they should consider weak positivity before proceeding.

Edited by Trey, 27 May 2017 - 09:49 AM.

[kat73]

I am glad that others are pondering this question, along with me.  I was made to feel ashamed of caring over such "splitting of hairs."  My onc is obviously frustrated by the constantly changing reporting systems, because when I asked, "so what is undetectable?" he answered, "zero."  Not holding my breath!

[cmljax]

so did you ask your onc what he meant by zero Kat?? It is frustrating because maintaining PCRU for 2 years is the standard for when my onc will consider further dose reduction or cessation, but I do not know if I have been there since I was .006, less than .003 or not there yet. I need to ask him to clarify and I intend to do just that.

[AdamJ]

Cmljax,  I believe the report will say "Negative" or something along those lines. Mine reports it as "Not Detected".

[hannibellemo]

Thanks for that, Frank. I will have my next PCR at Mayo (Rochester) in August and will be sure to have Dr. G explain the new reporting system to me at that time. It could be discouraging to show positive again if they have changed their testing or changed their reporting.

 

I always thought it was strange (disingenuous is a good term, Trey) that Mayo only reported to 0.01% while many others reporting negative were reporting at a much more sensitive rate.

[rcase13]

My lab here at Levine Cancer Institute has finally changed the way they report. They no longer stop at 0.01% IS. They now report the actual number. Apparently the test is more sensitive now as well. Luckily I was able to maintain PCRU. I told my doctor we all thought the 0.01% method of reporting was stupid.

[scuba]

Below is a very good summary describing "PCR" methodology in terms of process and sensitivity. The most accurate PCR method is the newer 'digital PCR' which does not require standards to compare against. It is an absolute measure giving a direct count of product produced (in our case bcr-abl) in comparison to the otheer PCR techniques. Most of us have Real-time PCR's conducted. Some labs may be converting to Digital PCR and not listing it on the report and may explain the change in sensitivity reported.

Real-time PCR vs. Traditional PCR vs. Digital PCR at a glance

	Digital PCR	Real-time PCR	Traditional PCR
Overview	Measures the fraction of negative replicates to determine absolute copies.	Measures PCR amplification as it occurs.	Measures the amount of accumulated PCR product at the end of the PCR cycles.
Quantitative?	Yes, the fraction of negative PCR reactions is fit to a Poisson statistical algorithm.	Yes, because data is collected during the exponential growth (log) phase of PCR when the quantity of the PCR product is directly proportional to the amount of template nucleic acid.	No, though comparing the intensity of the amplified band on a gel to standards of a known concentration can give you 'semi-quantitative' results.
Applications	Absolute quantification of viral load Absolute quantification of nucleic acid standards Absolute quantification of next-gen sequencing Libraries Rare allele detection Absolute quantification of gene expression Enrichment and separation of mixtures	Quantitation of gene expression Microarray verification Quality control and assay validation Pathogen detection SNP genotyping Copy number variation MicroRNA Analysis Viral quantitation siRNA/RNAi experiments	Amplification of DNA for: Sequencing Genotyping Cloning
Summary	Advantages of digital PCR: No need to rely on references or standards Desired precision can be achieved by increasing total number of PCR replicates Highly tolerant to inhibitors Capable of analyzing complex mixtures Unlike traditional qPCR, digital PCR provides a linear response to the number of copies present to allow for small fold change differences to be detected	Adavantages of real-time PCR: Increased dynamic range of detection No post-PCR processing Detection is capable down to a 2-fold change Collects data in the exponential growth phase of PCR An increase in reporter fluorescent signal is directly proportional to the number of amplicons generated The cleaved probe provides a permanent record amplification of an amplicon	Disadvantages of traditional PCR: Poor Precision Low sensitivity Short dynamic range < 2 logs Low resolution Non-automated Size-based discrimination only Results are not expressed as numbers Ethidium bromide for staining is not very quantitative Post-PCR processing

 

https://www.thermofi...qpcr-vs-digital-pcr-vs-traditional-pcr.html

 

[kat73]

cmljax - I haven't gotten one, so I don't know how it reads - presumably it says "not detected in either sample," or, what my onc implied, "0.000%" 

 

scuba - thanks - not sure my brain is up to yours in understanding all that, tho!  I think where most of us are frustrated (I could be wrong) is in the actual WAY the result is reported to us, regardless of how it has been reached, although of course that is the most important thing.

[Kali]

What does limit quantification of 0.0069% mean?
I keep getting non detectable however they report the detection limit of the test is one positive cell in 125,000 normal cells.

[kat73]

I share your frustration, Kali.  I think your takeaway is that they didn't see anything bad in your samples and therefore called you "undetectable," but they can't guarantee there is nothing in your entire body - zero - because the limits of the test's reliability only goes to 0.0069.  Meaning, below that, they may be able to detect something but their ability to measure it accurately is unreliable (lots of false positives.)

 

I have a hunch that various leading institutions are trying to change the politics, if you will, in this area.  Out of caution, I believe, they are worried the cessation cart is getting too much in front of the detection horse.  I think they're trying to reiterate that "undetectable" cannot be relied upon to mean, "cure" - as in, "I never have to take my TKI ever again."  This is, as I say, just a hunch, a feeling.  But I do sense some pushback from the science/medical establishment against a lot of the current happy talk about cessation.  Time will tell who is right, or how much right.

[campanula]

I have a hunch that various leading institutions are trying to change the politics, if you will, in this area.  Out of caution, I believe, they are worried the cessation cart is getting too much in front of the detection horse.  I think they're trying to reiterate that "undetectable" cannot be relied upon to mean, "cure" - as in, "I never have to take my TKI ever again." 

 

I agree, this is part of the story.  But I'm wondering if a bigger issue is standardizing treatment within the medical community.  I've seen on this forum that some doctors can seemingly overreact to a "jump" in results that is only a 0.001% difference and switch meds, etc.  So I think disclosing results to patients at the 4 log level (0.01%), where there is more accurate reporting, and declaring PCRU only when truly undetectable may be their way of standardizing treatment a bit more. 

[Kali]

Thank you Kat for clarifying what this means 😊

It does get confusing at times.

[kat73]

Good point, Campanula.

[Sneezy12]

I contacted one of the Clinical Pathologists at the Mayo Clinic Laboratory concerning my original post.
He indicated that they were merely reporting the 0.003% value to be consistent with the I.S., but that the Sensitivity remains the same. Frank

[cmljax]

So I guess some labs report undetectable if the reading is positive but below their cutoff - all still very confusing to me. For example, before Mayo changed their sensitivity reporting, would they have reported .006% as <.01% or would they have reported it as undetectable?