Dataset: Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity
The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With an extremely poor five-year survival rate...
The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With an extremely poor five-year survival rate of only 15%, identification of new therapeutic targets for EAC is of great importance. Here, we analyze the mutation spectra from the whole exome sequencing of 149 EAC tumors/normal pairs, 15 of which have also been subjected to whole genome sequencing. We identify a novel mutational signature in EACs defined by a high prevalence of A to C transversions at Ap*A dinucleotides. Statistical analysis of the exome data identified 26 genes that are mutated at a significant frequency. Of these 26 genes, only four (TP53, CDKN2A, SMAD4, and PIK3CA) have been previously implicated in EAC. The novel significantly mutated genes include several chromatin modifying factors and candidate contributors to EAC: SPG20, TLR4, ELMO1, and DOCK2. Notably, functional analyses of EAC-derived mutations in ELMO1 increase cellular invasion. Therefore, we suggest a new hypothesis about the potential activation of the RAC1 pathway to be a contributor to EAC tumorigenesis. The study aimed to analyze 150 primary, human esophageal adenocarcinoma samples by whole genome and whole exome sequencing (which will be deposited to dbGAP following the TCGA practice). RNA expression data was used to determine gene expression in 14 of the samples analyzed by whole genome sequencing. No normals were analyzed.
- Dec.12, 2014
- Jul.12, 2014
|Sample||PACK YEARS||PATHOLOGICAL T||AGE||A MUTATIONS||SEX||SMOKING STATUS||NON-SILENT MUTATION RATE PER MB WES||PATHOLOGICAL N||S ASSOCIATED||TUMOR GRADE|
|GSM103835||not specified||T1b||68||0.06||female||no||8.35||not specified||yes||moderately|
|GSM1038345||not specified||T1b||78||0.09||male||no||4.19||not specified||yes||moderately|
|GSM1038342||not specified||T1b||81||0.12||male||no||3.93||not specified||yes||moderately|
|GSM103834||not specified||T1b||58||0.05||male||no||3.49||not specified||yes||moderately|