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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
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Genes Samples CDS Mutation AA Mutation
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Non-Mutant Genes Gene Id (COSG)
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Non-Mutant Samples Sample Id (COSS)
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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 gene expression and copy number variation data for this study. [more details]

Table Information

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The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

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Sample Gene Expression Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type Minor Allele Copy Number CN Segment Posn. Average Ploidy

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

2. For TCGA samples, the ASCAT algorithm was used to calculate the average ploidy.

3. For CGP samples, the PICNIC algorithm was used to calculate the average ploidy.

CNV
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