Integrative genomic analysis reveals cancer-associated mutations at diagnosis of CML in patients with high risk disease

Study ID Alternative Stable ID Type
EGAS00001003071 Other

Study Description

Genomic events associated with poor outcome in chronic myeloid leukemia (CML) are poorly understood. We performed whole exome sequencing, copy number variation and/or RNA-Seq for 65 patients to discover mutations at diagnosis and blast crisis (BC). Forty-six chronic phase patients with the extremes of outcome were studied at diagnosis. Cancer gene variants were detected in 15/27 patients (56%) with subsequent BC or poor outcome and in 3/19 optimal responders (16%), P=.007. Frequently mutated genes at diagnosis were ASXL1, IKZF1 and RUNX1. The methyltransferase SETD1B was a novel recurrently mutated gene. A novel class of variant associated with the Philadelphia translocation was detected at diagnosis in 11/46 patients (24%) comprising fusions and/or rearrangement of genes on the translocated chromosomes, with evidence of fragmentation, inversion and imperfect sequence reassembly. These were more frequent at diagnosis in patients with poor outcome: 9/27 (33%) versus 2/19 optimal responders (11%), P=.07. Thirty-nine patients were tested at BC and all had cancer gene variants, ... (Show More)

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
This dataset contains WES and RNA-Seq fastq files for 65 CML patient samples at various stages of disease progression.
Illumina HiSeq 2000,Illumina HiSeq 2500,NextSeq 500 183

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