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

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity.

Paper Id
COSP31475
Authors
Dulak AM,Stojanov P,Peng S,Lawrence MS,Fox C,Stewart C,Bandla S,Imamura Y,Schumacher SE,Shefler E,McKenna A,Carter SL,Cibulskis K,Sivachenko A,Saksena G,Voet D,Ramos AH,Auclair D,Thompson K,Sougnez C,Onofrio RC,Guiducci C,Beroukhim R,Zhou Z,Lin L,Lin J,Reddy R,Chang A,Landrenau R,Pennathur A,Ogino S,Luketich JD,Golub TR,Gabriel SB,Lander ES,Beer DG,Godfrey TE,Getz G and Bass AJ
Affiliation
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
Journal
Nature genetics 2013;45(5):478-86
ISSN:1546-1718
PUBMED:23525077
Abstract
The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a 5-year survival rate of ~15%, the identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole-exome sequencing of 149 EAC tumor-normal pairs, 15 of which have also been subjected to whole-genome sequencing. We identify a mutational signature defined by a high prevalence of A>C transversions at AA dinucleotides. Statistical analysis of exome data identified 26 significantly mutated genes. Of these genes, five (TP53, CDKN2A, SMAD4, ARID1A and PIK3CA) have previously been implicated in EAC. The new significantly mutated genes include chromatin-modifying factors and candidate contributors SPG20, TLR4, ELMO1 and DOCK2. Functional analyses of EAC-derived mutations in ELMO1 identifies increased cellular invasion. Therefore, we suggest the potential activation of the RAC1 pathway as a contributor to EAC tumorigenesis.
Paper Status
Curated
Genes Analysed
13996
Mutated Samples
149
Total No. of Samples
149
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