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

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

Paper Id
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
Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.
Nature 2012;488(7409):49-56
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
Genes Analysed
Mutated Samples
Total No. of Samples
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.

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