Identifying DNA Sequences Unique to Cancer Cells (SJ-21-0046)

St. Jude Reference #SJ-21-0046


Oncogenic fusions formed through chromosomal rearrangements are hallmarks of childhood cancer that define cancer subtype, predict outcome, persist through treatment, and can now be therapeutic targets as scientists at St. Jude Children’s Research Hospital comprehensively characterized oncogenic fusions in pediatric cancer, providing proof-of-principle for genetic engineering and gene editing therapies.

Researchers at St. Jude discovered this genome-editing- and etiology-based strategy for cancer therapy. The invention includes an algorithm for identifying cryptic exons arising from aberrant splicing unique to cancer cells and can be applied to fusion-positive cancer patients with neo-splicing that introduced cryptic exons. Because these neo-splice sites (or the cryptic exons) are not used in normal cells, therapies targeting these sites are expected to be nontoxic to normal cells and theoretically have an infinite therapeutic window. 

Clinical outcomes have explained why a small group of pediatric patients with relapsed acute myeloid leukemia (AML) had poor outcomes. Subtle differences in the oncogenic fusion mutations were discovered, which explained survival outcomes better than any existing clinical diagnostics. The result demonstrated that the tool can be used for clinical predictions, which will help physicians choose more personalized and effective treatments for patients in the future.


Cancer, oncogenic fusions, chromosomal rearrangements, subtype, outcome, persistence, genetic engineering, gene editing, genome-editing, etiology, algorithm, cryptic exons, aberrant splicing, fusion-positive, therapy. 

Granted patents or published applications

Pending US patent.

Related scientific references

Liu, Y., Klein, J., Bajpai, R. et al. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Nat Commun 14, 1739 (2023).

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