This tab shows an overview of the selected study/paper [more details]
Reference

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia.

Paper Id
COSP29664
Authors
Roberts KG,Morin RD,Zhang J,Hirst M,Zhao Y,Su X,Chen SC,Payne-Turner D,Churchman ML,Harvey RC,Chen X,Kasap C,Yan C,Becksfort J,Finney RP,Teachey DT,Maude SL,Tse K,Moore R,Jones S,Mungall K,Birol I,Edmonson MN,Hu Y,Buetow KE,Chen IM,Carroll WL,Wei L,Ma J,Kleppe M,Levine RL,Garcia-Manero G,Larsen E,Shah NP,Devidas M,Reaman G,Smith M,Paugh SW,Evans WE,Grupp SA,Jeha S,Pui CH,Gerhard DS,Downing JR,Willman CL,Loh M,Hunger SP,Marra MA and Mullighan CG
Affiliation
Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
Journal
Cancer cell 2012;22(2):153-66
ISSN:1878-3686
PUBMED:22897847
Abstract
Genomic profiling has identified a subtype of high-risk B-progenitor acute lymphoblastic leukemia (B-ALL) with alteration of IKZF1, a gene expression profile similar to BCR-ABL1-positive ALL and poor outcome (Ph-like ALL). The genetic alterations that activate kinase signaling in Ph-like ALL are poorly understood. We performed transcriptome and whole genome sequencing on 15 cases of Ph-like ALL and identified rearrangements involving ABL1, JAK2, PDGFRB, CRLF2, and EPOR, activating mutations of IL7R and FLT3, and deletion of SH2B3, which encodes the JAK2-negative regulator LNK. Importantly, several of these alterations induce transformation that is attenuated with tyrosine kinase inhibitors, suggesting the treatment outcome of these patients may be improved with targeted therapy.
Paper Status
Curated
Genes Analysed
67
Mutated Samples
9
Total No. of Samples
9
This tab shows genes with mutations in the selected study/paper [more details]
Genes Samples CDS Mutation AA Mutation
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Non-Mutant Genes Gene Id (COSG)
This tab shows samples without mutations in the selected study/paper [more details]
Non-Mutant Samples Sample Id (COSS)
This tab shows mutated samples in the selected study/paper [more details]
Sample Name Mutation Count
This tab shows non coding variant in the selected study/paper [more details]
Sample ID Sample Name ID NCV Annotation Zygosity Chromosome Genome start Genome stop Genome version Strand WT seq Mut seq
This tab shows the copy number variation data for this study. Only variants (classified as gain or loss) are listed. [more details]
CNV Gene Sample Position Minor Allele Copy Number Average Ploidy

1. N/A represents cases where average ploidy value is not available( mostly ICGC samples). For some TCGA samples where minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, Ascat algorithm is used to calculate the average ploidy.

3. For CGP samples, Picnic algorithm is used to calculate the average ploidy.

Type
This tab shows a table of count of samples having gain or loss for all genes [more details]
Gene Gain Samples Loss Samples Samples Tested
This tab shows the fusion mutations observed in this sample [more details]
Gene Sample Name Id Sample(COSS) CDS Mutation Somatic status Zygosity Validated Type