FISH probe & panel project: An overview

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Jess F Peterson Square Profile pic

Jess Peterson, M.D.

Associate Professor of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science
Consultant, Division of Hematopathology and Laboratory Genetics
Mayo Clinic, Rochester, Minnesota



Hello. My name is Dr. Jess Peterson, and I’m an associate professor of Lab Medicine and Pathology and director of the FISH Laboratory.

The FISH Laboratory has been working on a multifaceted project to update our hematology FISH menu to improve our test offerings. Today I’m going to talk about these changes to increase awareness, provide reasoning for the updates, and highlight some of the great things that are coming.


I have no financial disclosures to speak of.

Overview of changes to FISH testing

The three main overview changes that I will address today are the process of streamlining billing with the new FISH test orderables; the change to ACD for the preferred tube type; and what the updated FISH test offerings mean for ordering practices. With the FISH test ordering changes, I will touch base and provide examples of the new test offering structure and introduce new novel test offerings.

Streamlined billing

I’d like to start by discussing changes to our billing practices. In our previous component model, all billing and CPT coding was triggered independently. We have restructured our component billing into a bundled format in which all component parts will be held under a single test code. This updated approach allows for more streamlined billing and will also result in a significant reduction in reflex or additional bill-only test codes.

This restructured billing practice will provide a more consistent and streamlined billing approach for our clients, in addition to an increased understanding of test price and CPT code application.

ACD as preferred tube type

The second item for discussion addresses the change from heparin as our preferred tube type, to ACD. Genetic testing for hematologic neoplasms is broad and can include conventional chromosome analysis, FISH, chromosomal microarray studies and/or other molecular based assays, such as NGS. Replacing heparin with ACD tubes enables improved cross-testing capability, or compatibility that we frequently encounter in the laboratory.

WHY: Updated test offerings

In addition to the billing and tube type updates, there are some exciting changes coming to our hematology FISH menu. These changes were implemented to provide a targeted approach to correlate with patient needs and improve patient care, and to correlate with current guidelines, including NCCN and WHO. By taking the time and effort to evaluate and update the probe composition of our FISH panel offerings, we were able to thoughtfully consider utilization management and limit unnecessary testing. 

Several changes to our hematology FISH menu have been made, and I encourage you to review at your leisure. 

The most significant changes to our testing menu involve our acute leukemia panels. Instead of a general “one size fits all” FISH panel, we have created disease-specific FISH panels based on patient age. Adults are considered to be above 30 years of age, and pediatric patients are considered 30 years of age or younger. In addition, we offer specific FISH panels for our patients enrolled in the Children’s Oncology Group trials. Tailoring our FISH panels by disease and age maximizes our ability to detect abnormalities of clinical significance.

We have also built our diagnostic FISH panels to include appropriate reflex testing. For example, if we detect a KMT2A translocation, previously known as MLL, we will run the KMT2A dual-color, dual-fusion FISH probe sets that are appropriate for the specific disease and patient age. 

In addition to being able to order complete panels, it is also important to us that our clients have the option of being able to order individual probes. We created secondary build-your-own tests for each disease state in which limited probes can be ordered. FISH is an excellent method to monitor disease in patients with previously detected abnormalities and may only require the use of a single FISH probe set. In these situations, these new limited probe tests will be ideal.

An example – FISH probe and panel transition

Now I’d like to move on and show some specific examples of our FISH panels and how they have changed. 

We have already transitioned to this updated testing format for our CLL FISH testing, which went live in March of 2021. Using this as an example, the previous test ID CLLF was obsolete; this is the grayed-out row shown here. We replaced CLLF with CLLDF, the “D” standing for diagnostic, and CLLMF, the “M” standing for miscellaneous, or requiring the orderer to specify when ordering which probes should be run. 

The diagnostic panel test CLLDF is appropriate for the diagnostic CLL specimen and includes the entire panel shown here, as well as the reflexes to the IGH/BCL3 dual-color, dual-fusion FISH probe set if an IGH translocation is identified. 

The follow-up or build-your-own test CLLMF is ideal for clients interested in detecting specific abnormalities that are offered within the CLLDF panel. For example, a client could order CLLMF and specify the chromosome 12 FISH probe for a patient with a previously reported history of CLL with trisomy 12. 

An additional example – FISH probe and panel transition

One of the updated test forms that we will be offering includes FISH testing for B-lymphoblastic leukemia. The previous test ID, BALLF, will be replaced with BALAF, “A” standing for “adult”; BALPF, “P” standing for “pediatric”; and BALMF, “M” standing for miscellaneous. In addition, the “COGBF,” which already exists today, will remain as an orderable for those clients that enroll in COG trials. Each B-ALL FISH panel follows tiered testing that maximizes abnormality detection and efficiency gains. For example, the adult BALL FISH panel starts with BCR/ABL1 and CRLF2/IGH, dual-color, dual-fusion FISH probe sets. And they detect some of the most common abnormalities observed in adult B-ALL. Only if these abnormalities are normal would we proceed to the next tier of testing, and so forth. 

Like CLLMF, BALMF is available for clients to order individual FISH probes within any of the BALL FISH panels.

Launch of new and novel tests

We’re also excited to announce three new tests for our clients. First, we will be offering a chronic eosinophilia FISH panel. Per the 2017 WHO, myeloid and lymphoid neoplasms with eosinophilia and translocations of PDGFR Alpha, PDGFR Beta, FGFR1, and JAK2 have been described and may be amenable to targeted therapy. We have also included ABL1, as hematologic neoplasms with ABL1 translocations can also be accompanied by eosinophilia, such as CML.

Secondly, we will be offering a congenital infantile leukemia FISH panel that will be available for blood, bone marrow, and formalin-fixed paraffin embedded tissue specimens. This unique FISH panel targets recurrent chromosomal abnormalities observed in patients between birth and 18 months of age.

Lastly, we are excited to provide a B-lymphoblastic lymphoma FISH panel on formalin-fixed paraffin embedded tissue for pediatric and adult patients. With the exception of IKZF1 and CRLF2 gene regions, this comprehensive FISH panel detects recurrent chromosomal abnormalities described in B-LBL, or B-lymphoblastic lymphoma.

Thank you

We recognize that updates to testing affects our clients’ internal processes as well. Because of this, we combined all of these updates into one test change rather than several incremental changes.

I would like to thank you for your time and attention. We look forward to continuing to provide top-notch FISH testing in order for you to provide the best care for your patients. Please don’t hesitate to reach out to us if you have any questions. Thank you again. 


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This post was developed by our Education and Technical Publications Team.