The BCR-ABL1 FISH probe pair is designed to detect rearrangements involving regions of the human BCR (Breakpoint cluster region) locus, located on chromosome band 22q11.23, and of the human ABL1 gene on 9q34.12. One probe covers the entire BCR gene along with some upstream (5’) and downstream (3’) flanking untranslated genomic sequences. The probe overlaps the known major and minor breakpoints observed in the region. The second probe spans the complete ABL1 gene on 9q34.12, including the common breakpoint region upstream of exon 2, as well as adjacent 5’ and 3’ untranslated genomic sequences. The probe set is optimized to reveal the typical t(9;22)(q34;q11) translocation as well as other translocations between the two genes, in metaphase and interphase blood or bone marrow cells.

Fluorescence in situ hybridization (FISH) is a powerful technique developed to detect presence or absence, location, integrity and amount of genomic sequences in tissue samples or cells.^1-3 

The product of the human BCR gene, breakpoint cluster region (BCR) protein, also called BCR1, PHL or renal carcinoma antigen NY-REN-26, is a ubiquitously expressed serine/threonine kinase and GTPase-activating cytoplasmic enzyme.⁴ Despite intensive studies, the role of BCR in normal cell physiology is not yet known.

Named for mapping at a site of frequent chromosome breaks, three breakpoint cluster regions within the BCR gene have been characterized to date: major (M-bcr), minor (m-bcr) and micro (μ-bcr). In addition to the most common fusion partner, ABL1, other translocation partners have been found in rarer leukemia subtypes.^5,6

ABL1 (Abelson murine leukemia viral oncogene homolog 1, also called c-ABL, JTK7, p150) is a cytoplasmic and nuclear tyrosine kinase involved in a variety of cellular processes including migration, adhesion, differentiation and apoptosis. It is also an important component of the T-cell receptor signaling system and required for T-cell development and function.⁷

Normally present in a passive state, ABL1 is found activated in myeloproliferative disorders as well as in lung and breast and other tumors. Activation in leukemias is most often resulting from fusion with BCR, but fusion to other partners has been reported.^8-11

BCR-ABL1 and Leukemia 

The t(9;22)(q34;q12) reciprocal translocation between BCR and ABL1 leads to a lengthened chromosome 9 (9q+) and a shortened chromosome 22 (der(22), 22-), also called Philadelphia-chromosome (Ph, Ph1). Discovered in 1960, it is a hallmark of chronic myelogenous leukemia (CML) and was the first consistent genetic abnormality identified in any human cancer.^12-15

The fusion combines varying portions of the 5’- part of BCR with the 3’-part (exons 2-11) of ABL1 and leads to the production of a fusion protein in which the tyrosine kinase of ABL is constitutively activated.

The Philadelphia chromosome is present in virtually all CML cases.¹⁶ However, it is also found in a subset of adult and pediatric acute lymphoblastic leukemia (ALL) and sometimes in acute myelogenouse leukemia (AML) and other malignancies such as the very rare chronic neutrophilic leukemia (CNL).

In addition to FISH analysis, the BCR-ABL1 fusion can be detected also by immunocytochemistry and qualitative or quantitative PCR methods. While the latter have found increasing use in isotype discrimination and in measuring low levels of minimal residual disease or major molecular response, FISH testing is the gold standard for initial diagnosis, prognosis and disease monitoring in CML and ALL.^17,18

In the past, combinations of chemotherapeutic agents, cytokines and steroids have been used as treatments to manage chronic phase CML. In recent years, however, the therapy of CML has been revolutionized by the development of competitive inhibitors that specifically target the constitutively activated ABL1 kinase. The first of these drugs, imatinib, was approved in 2001, found to be well tolerated and provide superior treatment results in a large number of patients.^19-23 More potent second (nilotinib, dasatinib) and third (bosutinib, flumatinib, panatinib) generation inhibitors have been developed for use in patients resistant to or intolerant of imatinib.^24-27

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