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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
EGAS00001000081 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
EGAF00000064074 bam 10.1 GB
EGAF00000064076 bam 10.4 GB
EGAF00000064077 bam 9.8 GB
EGAF00000064078 bam 10.9 GB
EGAF00000064079 bam 10.7 GB
EGAF00000064080 bam 11.4 GB
EGAF00000064081 bam 9.8 GB
EGAF00000064082 bam 10.6 GB
EGAF00000064084 bam 10.3 GB
EGAF00000064085 bam 11.7 GB
EGAF00000064086 bam 10.0 GB
EGAF00000064088 bam 6.7 GB
EGAF00000064089 bam 10.2 GB
EGAF00000064090 bam 8.5 GB
EGAF00000064091 bam 10.2 GB
EGAF00000064093 bam 8.7 GB
EGAF00000064094 bam 10.9 GB
EGAF00000064095 bam 9.8 GB
EGAF00000064096 bam 10.5 GB
EGAF00000064097 bam 10.4 GB
EGAF00000064098 bam 11.5 GB
EGAF00000064099 bam 10.6 GB
22 Files (223.8 GB)