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Background The Cancer Gename Atlas (TCGA) is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of genome analysis technologies including colon adenocarcinoma (COAD).Methods We retrieved the TCGA COAD level 1 data published on May 8, 2014 with Nexus 7.5, which included copy number aberration (CNA) from Affymetrix SNP6 and sequence variation from exome sequencing.Then, we classified COAD into prognostic groups to determine correlates of subtypes that may be biologically significant.Results We identified frequent (>35%) copy number gains of chromosomes 7, 8q, 13 and 20p, and losses of chromosomes 8p, 17p, and 18.Mutation of Kras and Braf were observed in 34.94% and 26.6% of patients.Copy number profiles varied significantly between hypermutable and non-hypermutable samples.Potential chromothriptic events were also observed within the COAD dataset.Conclusions Molecular stratification of patients with COAD may provide opportunities for the development of new treatment modalities.