Read Trey's link above (CML Testing Explained). It's a very good summary of the terms.
Answering your questions regarding Rabbits:
The Rabbit is the Leukemia cell. They are one in the same in my analogy above. The Leukemia cell contains the Philadelphia chromosome. The FISH test is looking for Leukemia Cells (Ph+ cells) as seen under a microscope.
Leukemia cells make stuff. Specifically, they make bcr-abl messenger RNA transcripts. The transcripts are the rabbit poop in my analogy above. Transcripts are measured using polymerase chain reaction process (PCR) to enhance the transcripts detection. The detection is done using machines to measure the amount of transcripts.
What's interesting is that a single leukemia cell can make little or a lot of transcripts. That is partially why PCR testing can be so problematic. It is possible for a person to have a low FISH or even zero FISH, but still have high PCR numbers. And likewise, it is possible for a person to have high FISH, but relatively low PCR numbers. Dr. Cortes believes that zero FISH and how long it takes to get there is an excellent prognosticator - more so than PCR. Because at the end of the day, it is the number of Rabbits that cause problems, not their poop. He doesn't want to see Rabbit reproduction. He doesn't want to see expansion of the Leukemia cells.
When Leukemia cells get very low in number (way below detection by FISH), PCR will tend to be very low also. It is at that point that Dr. Cortes told me that PCR to him is the canary in the mine shaft. He uses PCR to see if the first signs of trouble are beginning again (i.e. PCR starts to go up). If he sees a trend of increasing PCR's, he will the re-test for actual cells using FISH or even go back into the bone marrow. A several log increase in PCR would be cause for concern that response to the TKI drug is no longer working.
So PCR is a monitoring tool and as long as it is very low and stays there, we are in good shape and can expect that CML won't kill us as long as we keep taking our drugs. If PCR goes to zero (below detection) and stays there for several years, then we have a shot at a functional cure. There is a chance (4 in 10) that CML may have been eradicated or is otherwise under natural control by the body. Several people who follow this forum have stopped taking their TKI drug to test if they can stay disease free. I hope to join them.
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"