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RAG mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 Acute Lymphoblastic Leukemia (Whole_Genome_sequencing_data)

The ETV6-RUNX1 fusion gene, found in 25% of childhood acute lymphoblastic leukemia (ALL), is acquired in utero but requires additional somatic mutations for overt leukemia. We used exome and low-coverage whole-genome sequencing to characterize the critical secondary events associated with leukemic transformation. RAG-mediated deletions emerge as the dominant mutational process, accounting for at least 43% of genomic rearrangements and characterized by the presence of recombination signal sequence motifs near the breakpoints; incorporation of non-templated sequence at the junction and a ten-fold enrichment at promoters and enhancers of genes actively transcribed in early B-lineage development. Single-cell tracking shows that this mechanism is not restricted to one founder cell but is rather active throughout leukemic evolution. Integration of point mutation and rearrangement data identifies recurrent inactivation of ATF7IP and MGA as two new tumor suppressor genes.Thus, a remarkably parsimonious mutational process transforms ETV6-RUNX1 lymphoblasts, striking promoters and enhancers of the genes that normally control B-cell differentiation.

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001000058 Cancer Genomics

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00000065278 bam 11.8 GB
EGAF00000065280 bam 14.8 GB
EGAF00000065281 bam 14.2 GB
EGAF00000098568 bam 41.6 GB
EGAF00000098569 bam 41.1 GB
EGAF00000098570 bam 41.3 GB
EGAF00000098571 bam 42.4 GB
EGAF00000101649 bam 31.6 GB
EGAF00000103257 bam 15.3 GB
EGAF00000103258 bam 21.0 GB
EGAF00000104782 bam 15.7 GB
EGAF00000104783 bam 43.4 GB
EGAF00000117410 bam 32.9 GB
13 Files (367.1 GB)