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

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

Paper Id
COSP27921
Authors
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
Affiliation
Department of Computational Biology and Bioinformatics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
Journal
Nature 2012;481(7380):157-63
ISSN:1476-4687
PUBMED:22237106
Abstract
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
Curated
Genes Analysed
227
Mutated Samples
15
Total No. of Samples
15
This tab shows genes with mutations in the selected study/paper [more details]
Genes Samples CDS Mutation AA Mutation
This tab shows genes without mutations in the selected study/paper [more details]
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 gene expression and copy number variation data for this study. [more details]

Table Information

Hide

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.

Click here to include all copy number data. For more detailed information about copy number data and gain/loss definitions click here.

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 a summary table with counts (number of samples) for CNV gain/loss and under/over expression for all genes. [more details]

The results shown in this table are derived from all copy number data. This includes non-numeric data with descriptive definitions of gain/loss.

  Copy Number Expression
Gene Gain Loss Tested Over Under 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