Characterization of the translocation breakpoint sequences of two DEK‐CAN fusion genes present in t(6;9) acute myeloid leukemia and a SET‐CAN fusion gene found in a case of acute undifferentiated leukemia

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Abstract
The t(6;9) associated with a subtype of acute myeloid leukemia (AML) was shown to generate a fusion between the 3′ part of the CAN gene on chromosome 9 and the 5′ part of the DEK gene on chromosome 6. The same part of the CAN gene appeared to be involved in a case of acute undifferentiated leukemia (AUL) as well, where it was fused to the SET gene. Genomic sequences around the translocation breakpoint were determined in two t(6;9) samples and in the case of the SET-CAN fusion. Although coexpression of myeloid markers and terminal deoxynucleotidyl transferase was shown to be one of the characteristics of t(6;9) AML, no addition of random nucleotides at the translocation breakpoint could be found. In addition, the breakpoint regions did not reveal heptamer-nonamer sequences, purine-pyrimidine tracts, a chi-octamer motif, or Alu repeats. The sequence in which the translocation breakpoints occurred was enriched in A/T. Notably, the specific introns in which clustering of breakpoints occurs in DEK and CAN both contain a LINE-1 element. As LINE-1 elements occur with a moderate frequency in the human genome, the presence of such an element in both breakpoint regions may be more than coincidental and may play a role in the translocation process.