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Characterisation of the genomic landscape of CRLF2-d ALL

To determine the clinical and genetic landscape of CRLF2 deregulated acute lymphoblastic leukaemia (CRLF2-d ALL). We identified 172 patients with a CRLF2 rearrangement treated on either the UKALL2003 trial for children and adolescents (1-24 years) or the UKALLXII trial for adolescents and adults (15-59 years). Genomic technologies from conventional karyotyping, and FISH through to whole genome and exome sequencing were used to characterise the genomes of patients with CRLF2-d ALL. This is the largest study to date to investigate the genomic landscape of CRLF2-d ALL and define CRLF2-d as a unique subgroup of B-other ALL. We have confirmed the high incidence of CRLF2-d in Down syndrome-ALL and demonstrated the co-existence of CRLF2-d with other primary chromosomal rearrangements, suggesting that in these patients CRLF2-d can be a secondary genetic abnormality. Other defining features included enrichment of IKZF1, BTG1 and ADD3 deletions in IGH-CRLF2 patients and specific chromosomal gains seen at much higher frequencies than B-other ALL . We report recurrent established and new co-operating abnormalities and the novel involvement of USP9X and DDX3X in CRLF2-d ALL. It is clear from these data that CRLF2-d ALL is heterogenoeus, requiring a combination of genetic abnormalities in functionally relevent genes, to work alongside the deregulated expression of CRLF2 in order to initiate and drive leukaemogenesis in this subtype. Although the functional relevance of many of the abnormalities presented here are currently unknown, many are likely to activate alternate pathways or sensitize patients to current therapies.

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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
EGAS00001000080 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
EGAF00000058100 bam 16.9 GB
EGAF00000058101 bam 18.2 GB
EGAF00000058102 bam 15.5 GB
EGAF00000058103 bam 14.6 GB
EGAF00000058104 bam 16.4 GB
EGAF00000058105 bam 16.4 GB
EGAF00000058108 bam 17.2 GB
EGAF00000058109 bam 15.7 GB
EGAF00000058110 bam 22.4 GB
EGAF00000058111 bam 21.2 GB
EGAF00000058112 bam 14.2 GB
EGAF00000058113 bam 14.1 GB
EGAF00000058114 bam 17.2 GB
EGAF00000058115 bam 14.9 GB
EGAF00000058116 bam 12.9 GB
EGAF00000058117 bam 12.9 GB
EGAF00000058120 bam 18.9 GB
EGAF00000058121 bam 18.9 GB
EGAF00000058122 bam 9.9 GB
EGAF00000058123 bam 10.1 GB
EGAF00000058124 bam 13.7 GB
EGAF00000058125 bam 14.0 GB
22 Files (346.4 GB)