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Updated: Jul 11, 2026
Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
Molecular characterization of a rare MLL-AF4 (MLL-AFF1) fusion rearrangement in infant leukemia
Susana Bizarro1, Nuno Cerveira, Cecília Correia
1Department of Genetics, Portuguese Oncology Institute, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal.
Abstract:
The t(4;11)(q21;q23) involving the genes MLL and AF4 (alias for AFF1) is detected in 50-70% of infant leukemia. We characterize at both the DNA and RNA level a rare MLL-AF4 fusion transcript identified in a 15-month-old girl with acute lymphoblastic leukemia. Direct sequence analysis of the reverse transcriptase-polymerase chain reaction product showed an in-frame fusion between MLL exon 9 and AF4 exon 6. We further demonstrated that the genomic breakpoints were located 1,553 bp downstream of MLL exon 9 and 1,239 bp upstream of AF4 exon 6. Four Alu repeats were detected in MLL intron 9 and two Alu repeats and one LINE1 repetitive element were identified downstream of AF4 exon 5. Finally, a 9-bp polypurine (A) tract and an 8-bp polypyrimidine (T) tract were found flanking the translocation breakpoint. In summary, we have characterized at both the RNA and the DNA level a rare MLL-AF4 fusion variant that was presumably mediated by Alu repeats or polypurine and polypyrimidine tracts located in the vicinity of genomic breakpoints.
Insights
This study details a rare MLL-AF4 fusion transcript in infant acute lymphoblastic leukemia. The genetic breakpoints were linked to repetitive DNA elements, offering insights into leukemia development.
Area of Science:
- Molecular Biology
- Genetics
- Oncology
Background:
- The MLL-AF4 fusion gene, resulting from the t(4;11) translocation, is a common driver in infant leukemia.
- Understanding the precise molecular mechanisms of MLL-AF4 fusion formation is crucial for targeted therapies.
Purpose of the Study:
- To characterize the DNA and RNA features of a rare MLL-AF4 fusion transcript in infant acute lymphoblastic leukemia.
- To investigate the genomic breakpoints and potential mediating factors of this specific MLL-AF4 fusion variant.
Main Methods:
- Reverse transcriptase-polymerase chain reaction (RT-PCR) for transcript analysis.
- Direct DNA sequencing to identify fusion gene sequences and genomic breakpoints.
- Analysis of repetitive elements and sequence tracts near breakpoints.
Main Results:
- An in-frame MLL-AF4 fusion transcript was identified, joining MLL exon 9 and AF4 exon 6.
- Genomic breakpoints were precisely mapped within MLL intron 9 and AF4 intron 5.
- Alu repeats and polypurine/polypyrimidine tracts were found near the breakpoints, suggesting a role in the translocation.
Conclusions:
- A rare MLL-AF4 fusion variant was characterized at both RNA and DNA levels.
- Repetitive DNA elements and specific sequence tracts likely mediated the t(4;11) translocation in this case.
- This detailed characterization contributes to understanding the heterogeneity of MLL-AF4 fusions in infant leukemia.
