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

The genetic landscape of high-risk neuroblastoma.

Paper Id
COSP30850
Authors
Pugh TJ,Morozova O,Attiyeh EF,Asgharzadeh S,Wei JS,Auclair D,Carter SL,Cibulskis K,Hanna M,Kiezun A,Kim J,Lawrence MS,Lichenstein L,McKenna A,Pedamallu CS,Ramos AH,Shefler E,Sivachenko A,Sougnez C,Stewart C,Ally A,Birol I,Chiu R,Corbett RD,Hirst M,Jackman SD,Kamoh B,Khodabakshi AH,Krzywinski M,Lo A,Moore RA,Mungall KL,Qian J,Tam A,Thiessen N,Zhao Y,Cole KA,Diamond M,Diskin SJ,Mosse YP,Wood AC,Ji L,Sposto R,Badgett T,London WB,Moyer Y,Gastier-Foster JM,Smith MA,Auvil JM,Gerhard DS,Hogarty MD,Jones SJ,Lander ES,Gabriel SB,Getz G,Seeger RC,Khan J,Marra MA,Meyerson M and Maris JM
Affiliation
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Journal
Nature genetics 2013;45(3):279-84
ISSN:1546-1718
PUBMED:23334666
Abstract
Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%. To determine the spectrum of somatic mutation in high-risk neuroblastoma, we studied 240 affected individuals (cases) using a combination of whole-exome, genome and transcriptome sequencing as part of the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) initiative. Here we report a low median exonic mutation frequency of 0.60 per Mb (0.48 nonsilent) and notably few recurrently mutated genes in these tumors. Genes with significant somatic mutation frequencies included ALK (9.2% of cases), PTPN11 (2.9%), ATRX (2.5%, and an additional 7.1% had focal deletions), MYCN (1.7%, causing a recurrent p.Pro44Leu alteration) and NRAS (0.83%). Rare, potentially pathogenic germline variants were significantly enriched in ALK, CHEK2, PINK1 and BARD1. The relative paucity of recurrent somatic mutations in neuroblastoma challenges current therapeutic strategies that rely on frequently altered oncogenic drivers.
Paper Status
Curated
Genes Analysed
4817
Mutated Samples
238
Total No. of Samples
254
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