Original articleGeneral thoracicComparative Genomics of Esophageal Adenocarcinoma and Squamous Cell Carcinoma
Section snippets
Esophageal Adenocarcinoma Copy Number Data
We obtained Affymetrix 250K Sty GeneChip data from 73 patients with EAC originally published as part of a study by Berouhkim and associates [8] from the authors. Tumor data were normalized to a baseline reference file that was created from matched normal subjects. Additionally, we included our own Affymetrix 6.0 SNP array data from 116 EACs from patients treated at the University of Pittsburgh Medical Center from 2002 through 2008. The baseline reference file for this population was created
Common Regions of Aberrations
Analyses of CN data from 70 ESCC and 189 EAC samples resulted in at least 18 regions of gain and 14 regions of loss that occur in both ESCC and EAC at similar frequencies (p < 0.05 by Fisher's exact test; Table 1). These changes include previously reported cancer loci including gains (VEGFA [6p], EGFR [7p], CDK6 [7q21], MET [7q31], KRAS [12p], ERBB2 [17q12]) and losses (FHIT [3p], CSMDI [8p], and SMAD4 [18q]). We also observed other regions of gain, such as on 1p, 1q, 6p, 7q22, 8p, 10q, 11q,
Comment
We have performed a comparative genomic analysis of the largest cohort of EAC and ESCC samples and at the highest resolution to date. We found considerable similarity between these two tumor types but also many focal regions of DNA amplification or loss that are more frequent in one histologic type than in the other. This confirms some findings from smaller studies reported previously [11, 12], but our considerably larger sample size allows us to more precisely define regions, accurately
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