Break Apart Probe

Order Number
Package Size
100 µl (10 Tests)



XL KMT2A BA consists of an orange-labeled probe hybridizing proximal to the KMT2A gene region at 11q23.3 extending into the gene up to intron 24 and a green-labeled probe hybridizing distal to the KMT2A gene region at 11q23.3 extending into the gene up to intron 20 and thus overlapping each other for 3.4kb (GRCh37/hg19).

Probe maps are created in accordance with the intended purpose of the product. Solid colored bars do not necessarily indicate that the probe fully covers the indicated genomic region. Therefore, caution is advised when interpreting results generated through off-label use. Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Further information is available on request.

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Clinical Details

The KMT2A (fomerly MLL) gene, located on chromosome 11q23, is rearranged in about 10% of all acute leukemia patients. Most of them suffer from acute lymphoblastic leukemia (ALL) or acute myeloid leukemia (AML). Only a minority shows mixed lineage leukemia which has given the gene its original name ´MLL´. In infants, the incidence of KMT2A rearrangements in leukemia is 70-80%. KMT2A encodes a nuclear protein with methyltransferase activity and is part of multiprotein complexes involved in the regulation of target genes essential during early development and hematopoiesis. Today, more than 80 translocation partners of KMT2A have been identified. Translocations are resulting in in-frame fusions between the KMT2A part N-terminal to the break point cluster region and the respective fusion partners. The most common translocation partners in KMT2A associated leukemia are, in the order of their prevalence, AFF1, MLLT3, MLLT1, MLLT10, ELL and AFDN. Fusion genes may also be the result of an insertion of genetic material including portions of KMT2A into other chromosomal locations. Some examples of fusion genes reported as a result of this mechanism are KMT2A-AFF1, KMT2A-MLLT3 and KMT2A-MLLT10.
The proven MetaSystems XL MLL plus D-5060-100-OG is designed to detect breaks in the KMT2A gene region. Featuring a new gene covering design, XL KMT2A BA D-5090-100-OG allows the detection of cryptic insertion of portions of KMT2A into other chromosomes as an added benefit, provided that the inserted DNA fragment is in the size range detectable by fluorescence microscopy.

Clinical Applications

  • Acute Lymphoblastic Leukemia (ALL)
  • Acute Myelogenous Leukemia (AML)
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XL KMT2A BA hybridized to bone marrow cells, one aberrant cell is shown. A cryptic insertion of KMT2A is observed generating a signal pattern of two orange-green colocalization/fusion signals and one additional orange signal.

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Expected Patterns

Expected Pattern 1

Normal Cell:
Two green-orange (2GO) colocalization/fusion signals.

Expected Pattern 2

Aberrant Cell (typical results):
One green-orange colocalization/fusion signal (1GO), one separate green (1G) and orange (1O) signal each resulting from a chromosome break in the respective locus. Translocations with breakpoints within the KMT2A breakpoint cluster region result in a small orange split signal remaining with the separated green signal. The residual orange signal is significantly smaller than the separated orange signal and might even be invisible.

Expected Pattern 3

Aberrant Cell (typical results):
Two green-orange colocalization/fusion signals (2GO) and one separate usually small orange (1O) signal indicating an insertion of the respective genomic region to an unknown chromosome.

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  • Soler et al (2008) Cancer Genet Cytogenet 183:53-59
  • Meyer et al (2013) Leukemia 27:2165-2176
  • Winters and Bernt (2017) Front Pediatr 5:4.doi:10.3389/fped.2017.00004