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

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Paper Id
COSP29480
Authors
Northcott PA,Shih DJ,Peacock J,Garzia L,Morrissy AS,Zichner T,Stütz AM,Korshunov A,Reimand J,Schumacher SE,Beroukhim R,Ellison DW,Marshall CR,Lionel AC,Mack S,Dubuc A,Yao Y,Ramaswamy V,Luu B,Rolider A,Cavalli FM,Wang X,Remke M,Wu X,Chiu RY,Chu A,Chuah E,Corbett RD,Hoad GR,Jackman SD,Li Y,Lo A,Mungall KL,Nip KM,Qian JQ,Raymond AG,Thiessen NT,Varhol RJ,Birol I,Moore RA,Mungall AJ,Holt R,Kawauchi D,Roussel MF,Kool M,Jones DT,Witt H,Fernandez-L A,Kenney AM,Wechsler-Reya RJ,Dirks P,Aviv T,Grajkowska WA,Perek-Polnik M,Haberler CC,Delattre O,Reynaud SS,Doz FF,Pernet-Fattet SS,Cho BK,Kim SK,Wang KC,Scheurlen W,Eberhart CG,Fèvre-Montange M,Jouvet A,Pollack IF,Fan X,Muraszko KM,Gillespie GY,Di Rocco C,Massimi L,Michiels EM,Kloosterhof NK,French PJ,Kros JM,Olson JM,Ellenbogen RG,Zitterbart K,Kren L,Thompson RC,Cooper MK,Lach B,McLendon RE,Bigner DD,Fontebasso A,Albrecht S,Jabado N,Lindsey JC,Bailey S,Gupta N,Weiss WA,Bognár L,Klekner A,Van Meter TE,Kumabe T,Tominaga T,Elbabaa SK,Leonard JR,Rubin JB,Liau LM,Van Meir EG,Fouladi M,Nakamura H,Cinalli G,Garami M,Hauser P,Saad AG,Iolascon A,Jung S,Carlotti CG,Vibhakar R,Ra YS,Robinson S,Zollo M,Faria CC,Chan JA,Levy ML,Sorensen PH,Meyerson M,Pomeroy SL,Cho YJ,Bader GD,Tabori U,Hawkins CE,Bouffet E,Scherer SW,Rutka JT,Malkin D,Clifford SC,Jones SJ,Korbel JO,Pfister SM,Marra MA and Taylor MD
Affiliation
Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.
Journal
Nature 2012;488(7409):49-56
ISSN:1476-4687
PUBMED:22832581
Abstract
Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-β signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.
Paper Status
Curated
Genes Analysed
5
Mutated Samples
63
Total No. of Samples
75
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

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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.

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