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The mutational landscape of adenoid cystic carcinoma.

Paper Id
Ho AS,Kannan K,Roy DM,Morris LG,Ganly I,Katabi N,Ramaswami D,Walsh LA,Eng S,Huse JT,Zhang J,Dolgalev I,Huberman K,Heguy A,Viale A,Drobnjak M,Leversha MA,Rice CE,Singh B,Iyer NG,Leemans CR,Bloemena E,Ferris RL,Seethala RR,Gross BE,Liang Y,Sinha R,Peng L,Raphael BJ,Turcan S,Gong Y,Schultz N,Kim S,Chiosea S,Shah JP,Sander C,Lee W and Chan TA
Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
Nature genetics 2013;45(7):791-8
Adenoid cystic carcinomas (ACCs) are among the most enigmatic of human malignancies. These aggressive salivary gland cancers frequently recur and metastasize despite definitive treatment, with no known effective chemotherapy regimen. Here we determined the ACC mutational landscape and report the exome or whole-genome sequences of 60 ACC tumor-normal pairs. These analyses identified a low exonic somatic mutation rate (0.31 non-silent events per megabase) and wide mutational diversity. Notably, we found mutations in genes encoding chromatin-state regulators, such as SMARCA2, CREBBP and KDM6A, suggesting that there is aberrant epigenetic regulation in ACC oncogenesis. Mutations in genes central to the DNA damage response and protein kinase A signaling also implicate these processes. We observed MYB-NFIB translocations and somatic mutations in MYB-associated genes, solidifying the role of these aberrations as critical events in ACC. Lastly, we identified recurrent mutations in the FGF-IGF-PI3K pathway (30% of tumors) that might represent new avenues for therapy. Collectively, our observations establish a molecular foundation for understanding and exploring new treatments for ACC.
Paper Status
Genes Analysed
Mutated Samples
Total No. of Samples
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Genes Samples CDS Mutation AA Mutation
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Table Information


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
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 FATHMM-MKL
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.

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.

This table lists the samples in the selected study which have low/high methylation for each gene. [more details]

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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