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

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.

Paper Id
Zhang J,Ding L,Holmfeldt L,Wu G,Heatley SL,Payne-Turner D,Easton J,Chen X,Wang J,Rusch M,Lu C,Chen SC,Wei L,Collins-Underwood JR,Ma J,Roberts KG,Pounds SB,Ulyanov A,Becksfort J,Gupta P,Huether R,Kriwacki RW,Parker M,McGoldrick DJ,Zhao D,Alford D,Espy S,Bobba KC,Song G,Pei D,Cheng C,Roberts S,Barbato MI,Campana D,Coustan-Smith E,Shurtleff SA,Raimondi SC,Kleppe M,Cools J,Shimano KA,Hermiston ML,Doulatov S,Eppert K,Laurenti E,Notta F,Dick JE,Basso G,Hunger SP,Loh ML,Devidas M,Wood B,Winter S,Dunsmore KP,Fulton RS,Fulton LL,Hong X,Harris CC,Dooling DJ,Ochoa K,Johnson KJ,Obenauer JC,Evans WE,Pui CH,Naeve CW,Ley TJ,Mardis ER,Wilson RK,Downing JR and Mullighan CG
Department of Computational Biology and Bioinformatics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
Nature 2012;481(7380):157-63
Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.
Paper Status
Genes Analysed
Mutated Samples
Total No. of Samples
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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 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.

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