At the moment probably not, but in the future we could expect some changes. Whereas in the previous 2006 and 2009 editions, the ELN recommendations for CML treatment and monitoring were indicating the cytogenetics analysis as the main method to evaluate the response to TKI treatment of CML patients at early times points (3 and 6 months), the 2013 edition recently published suggests that a strict molecular monitoring at these time points is also highly recommended and to be performed with a standardized method of RQ PCR. This is a consequence of a number of studies that have provided evidence that a BCR-ABL level above 10% at 3 months or above 1% at 6 months is predictive of an inferior outcome in terms of PFS and of OS with a statistical significance and more predictive of a corresponding achievement of a PCyR response at 3 months or of a CCyR response at 6 months.
A) Within this context, the labs are expected to focus their efforts to standardize with great precision the detection of these levels of BCR-ABL in addition to MMR, that according to ELN 2013 recommendations still remains a step to be achieved within 12 months in order to have an optimal response. This would probably be more probably achieved using the Cepheid machine, that could indeed present several advantages with respect to the more traditional methods, like an decreased need of sample exchanges to establish the conversion factor of an individual lab and a more rapid availability of the results of the analysis, because the entire process requires only 2-3 hours. The latter is a important aspect to be considered, because the BCR-ABL level at 3 or 6 months is expected to be the basis to drive a possible change in the therapy.
B) On the other side, a great deal of attention has been recently focused of the precise definition of minimal amounts of residual disease (MR4, MR4.5 and MR5) as this could represent the basis to enroll the patients in trial leading the CML patients to treatment discontinuation. This could be ideally achieved with new methods of digital PCR, that do not need a control gene (and therefore no need of standardization) and could detect the residual copies of BCR-ABL transcripts with great precision.

Were there any recent changes in the PCR process (lab, equipment or reagents used, or calculation process)?

again I refer you to the presentation. 2 additional chromosome abnormalities in a child. By the German and Italian data, this child was bad risk to begin with. Regardless of the reason this is happening now, he is in trouble. Before he goes acute, the allograft is the best option. There is not data to suggest playing around with additional TKIs will help

This is certainly a challenging problem. If adherence seems not to be a problem, then I would do nothing until you have repeated the RQ-PCR (very soon) and confirmed the substntial rise you have observed between March and June. If not confirmed then probably make no changes.

If confirmed it would indeed be worth doing a marrow aspirate and KD mutation analysis. Treatment options then include ponatinib and SCT, probably in that sequence.

I agree with Tim that strict molecular monitoring is essential and it is important also to check again for the presence of mutations. If and as soon as the BCR-ABL level will be above 1%, it is important also to perform BM aspiration in order to evaluate morphology as well as cytogenetics. In case of an emergence of a dasatinib resistant clone (even at the present dose) I would take in great consideration the SCT option, as I do not believe that ponatinib at this moment is available for pediatric cases and furthermore we do not have any information on its long-term effects on growth.

The presenting cytogenetics were of a major concern to begin with and the response to various drugs worrisome as well. As Tim suggested, there may be some mileage with dose or drug switches, but this kid is a ticking bomb for going acute. If there is a reasonable donor available, I would strongly favor an allograft. This is probably going to be necessary at some point in the future and the results of doing this in CP1 far exceed those of doing it in advanced disease whether or not CP2 can be achieved.