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Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations.

Paper Id
Pugh TJ,Weeraratne SD,Archer TC,Pomeranz Krummel DA,Auclair D,Bochicchio J,Carneiro MO,Carter SL,Cibulskis K,Erlich RL,Greulich H,Lawrence MS,Lennon NJ,McKenna A,Meldrim J,Ramos AH,Ross MG,Russ C,Shefler E,Sivachenko A,Sogoloff B,Stojanov P,Tamayo P,Mesirov JP,Amani V,Teider N,Sengupta S,Francois JP,Northcott PA,Taylor MD,Yu F,Crabtree GR,Kautzman AG,Gabriel SB,Getz G,Jäger N,Jones DT,Lichter P,Pfister SM,Roberts TM,Meyerson M,Pomeroy SL and Cho YJ
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
Nature 2012;488(7409):106-10
Medulloblastomas are the most common malignant brain tumours in children. Identifying and understanding the genetic events that drive these tumours is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma on the basis of transcriptional and copy number profiles. Here we use whole-exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas have low mutation rates consistent with other paediatric tumours, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were newly identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR and LDB1. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant, but not wild-type, β-catenin. Together, our study reveals the alteration of WNT, hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic β-catenin signalling in medulloblastoma.
Paper Status
Genes Analysed
Mutated Samples
Total No. of Samples
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Genes Samples CDS Mutation AA Mutation
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This is a whole exome/systematic screen paper and the negatives for this paper should be inferred.

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Non-Mutant Samples Sample Id (COSS)
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Sample Name Mutation Count
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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


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.

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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.

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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