Identifying novel genomic alterations in relapsed childhood B-ALL: a report from the Children's Oncology Group.

In relapsed childhood B-ALL, gain of the ETV6::RUNX1 fusion allele or an E5-E4 fusion transcript is linked to a higher risk of first relapse than E5-E3.

• Why it matters: Relapse in B-ALL often reflects therapy-resistant subclones, but subtype-specific genomic drivers are not fully defined for guiding treatment decisions.
• What they did: In the Children’s Oncology Group trial AALL1331, whole-genome and transcriptome sequencing of 288 patients (including diagnosis/first-relapse/germline trios and additional first-relapse samples) analyzed 41 second-relapse samples.
• The result: Subtype-level alterations explained 30% (n=55) of first relapses, and TCF3::PBX1/NT5C2 was linked to worse outcomes regardless of randomized arm.

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