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

Novel mutations target distinct subgroups of medulloblastoma.

Paper Id
COSP29055
Authors
Robinson G,Parker M,Kranenburg TA,Lu C,Chen X,Ding L,Phoenix TN,Hedlund E,Wei L,Zhu X,Chalhoub N,Baker SJ,Huether R,Kriwacki R,Curley N,Thiruvenkatam R,Wang J,Wu G,Rusch M,Hong X,Becksfort J,Gupta P,Ma J,Easton J,Vadodaria B,Onar-Thomas A,Lin T,Li S,Pounds S,Paugh S,Zhao D,Kawauchi D,Roussel MF,Finkelstein D,Ellison DW,Lau CC,Bouffet E,Hassall T,Gururangan S,Cohn R,Fulton RS,Fulton LL,Dooling DJ,Ochoa K,Gajjar A,Mardis ER,Wilson RK,Downing JR,Zhang J and Gilbertson RJ
Affiliation
1] St Jude Children's Research Hospital, Washington University Pediatric Cancer Genome Project, Memphis, Tennessee 38105, USA [2] Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [3] Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA [4].
Journal
Nature 2012
ISSN:1476-4687
PUBMED:22722829
Abstract
Medulloblastoma is a malignant childhood brain tumour comprising four discrete subgroups. Here, to identify mutations that drive medulloblastoma, we sequenced the entire genomes of 37 tumours and matched normal blood. One-hundred and thirty-six genes harbouring somatic mutations in this discovery set were sequenced in an additional 56 medulloblastomas. Recurrent mutations were detected in 41 genes not yet implicated in medulloblastoma; several target distinct components of the epigenetic machinery in different disease subgroups, such as regulators of H3K27 and H3K4 trimethylation in subgroups 3 and 4 (for example, KDM6A and ZMYM3), and CTNNB1-associated chromatin re-modellers in WNT-subgroup tumours (for example, SMARCA4 and CREBBP). Modelling of mutations in mouse lower rhombic lip progenitors that generate WNT-subgroup tumours identified genes that maintain this cell lineage (DDX3X), as well as mutated genes that initiate (CDH1) or cooperate (PIK3CA) in tumorigenesis. These data provide important new insights into the pathogenesis of medulloblastoma subgroups and highlight targets for therapeutic development.
Paper Status
Curated
Genes Analysed
2703
Mutated Samples
75
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 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.

Type
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