Two groups, we examined a number of clinical, pathological, and previously-defined

Two groups, we examined a number of clinical, pathological, and previously-defined molecular characteristics (CI 1011 site Figure 2a). Lymph node positivity was more common in the biliary-like group compared to the intestinal-like group (100 vs. 50 , p = 0.06). In contrast, there was no difference in other clinicopathological parameters such as the presence of a pre-existing adenoma or poorly differentiated histology. Molecular testing also showed no significant difference in the prevalence of mutations in KRAS, BRAF, or PIK3CA genes, or in MSI phenotype, between the two groups. Immunohistochemical analysis demonstrated positive CDX-2 expression in 83 of the intestinal-like group, but CDX-2 expression was also seen in 63 of the biliary-like group (p = 0.58). The factors best able to discriminate between the two ampullary subgroups were CK7+/CK202 immunohistochemical pattern (p,0.01) and histological subtype (p,0.01).Survival AnalysisAssociation between categorical clinical variables was determined by the Fisher’s exact test. Survival curves were generated using the Kaplan-Meier method and survival differences were determined with the log-rank test. The univariate Cox proportional hazards ZK-36374 site regression model for overall survival (OS) and relapse-free survival (RFS) tested age, histological grade, histological subtype, tumor stage, resection margin status, lymph node involvement, adjuvant treatment, and immunohistochemical variables. Cox proportional hazards models were fitted for multivariate analysis. After interactions between variables were examined, a backward stepwise procedure was used to derive the best-fitting model. Statistical analyses were performed using Stata MP version 10.1 and R version 2.12.0.Results Periampullary Adenocarcinoma Gene Expression ProfilingWe performed unsupervised hierarchical clustering upon all samples using all mRNA expression data (31,416 probesets), Figure 1a. This analysis identified two statistically different groups of periampullary carcinomas (p,0.01) with the ampullary carcinomas segregating into both groups. In order to further investigate these two ampullary subgroups and to directly compare ampullary carcinomas to non-ampullary periampullary carcinomas, we performed supervised hierarchical clustering analysis of the expression pattern of the genes (n = 133) that showed significant differences in expression between pancreatic and duodenal cases. This analysis identified three distinct groups (Figure 1b). Group 1 included all of the pancreatic carcinomas, and one duodenal carcinoma. This duodenal sample did not appear to be a misclassification as it demonstrated less than 1 mm invasion into the pancreas by histology and 100 tumor tissue on H E review of the frozen tissue sample. Groups 2 and 3 included the remaining duodenal tumors, and all of the ampullary tumors. The two extrahepatic cholangiocarcinomas included in the study also clustered together in Group 2. Review of the clinical histories found that the patients with ampullary and duodenal adenocarcinomas survived longer than patients with pancreatic or biliary adenocarcinomas (Figure 1c). However, the difference did not reach statistical significance (Logrank test for trend, p = 0.13). In contrast, we observed significant difference in overall survival when these same samples were analyzed according to their gene expression groupings (Figure 1d, Logrank test for trend, p = 0.02). Consistent with the preponderance of pancreatic tumors, the patients in.Two groups, we examined a number of clinical, pathological, and previously-defined molecular characteristics (Figure 2a). Lymph node positivity was more common in the biliary-like group compared to the intestinal-like group (100 vs. 50 , p = 0.06). In contrast, there was no difference in other clinicopathological parameters such as the presence of a pre-existing adenoma or poorly differentiated histology. Molecular testing also showed no significant difference in the prevalence of mutations in KRAS, BRAF, or PIK3CA genes, or in MSI phenotype, between the two groups. Immunohistochemical analysis demonstrated positive CDX-2 expression in 83 of the intestinal-like group, but CDX-2 expression was also seen in 63 of the biliary-like group (p = 0.58). The factors best able to discriminate between the two ampullary subgroups were CK7+/CK202 immunohistochemical pattern (p,0.01) and histological subtype (p,0.01).Survival AnalysisAssociation between categorical clinical variables was determined by the Fisher’s exact test. Survival curves were generated using the Kaplan-Meier method and survival differences were determined with the log-rank test. The univariate Cox proportional hazards regression model for overall survival (OS) and relapse-free survival (RFS) tested age, histological grade, histological subtype, tumor stage, resection margin status, lymph node involvement, adjuvant treatment, and immunohistochemical variables. Cox proportional hazards models were fitted for multivariate analysis. After interactions between variables were examined, a backward stepwise procedure was used to derive the best-fitting model. Statistical analyses were performed using Stata MP version 10.1 and R version 2.12.0.Results Periampullary Adenocarcinoma Gene Expression ProfilingWe performed unsupervised hierarchical clustering upon all samples using all mRNA expression data (31,416 probesets), Figure 1a. This analysis identified two statistically different groups of periampullary carcinomas (p,0.01) with the ampullary carcinomas segregating into both groups. In order to further investigate these two ampullary subgroups and to directly compare ampullary carcinomas to non-ampullary periampullary carcinomas, we performed supervised hierarchical clustering analysis of the expression pattern of the genes (n = 133) that showed significant differences in expression between pancreatic and duodenal cases. This analysis identified three distinct groups (Figure 1b). Group 1 included all of the pancreatic carcinomas, and one duodenal carcinoma. This duodenal sample did not appear to be a misclassification as it demonstrated less than 1 mm invasion into the pancreas by histology and 100 tumor tissue on H E review of the frozen tissue sample. Groups 2 and 3 included the remaining duodenal tumors, and all of the ampullary tumors. The two extrahepatic cholangiocarcinomas included in the study also clustered together in Group 2. Review of the clinical histories found that the patients with ampullary and duodenal adenocarcinomas survived longer than patients with pancreatic or biliary adenocarcinomas (Figure 1c). However, the difference did not reach statistical significance (Logrank test for trend, p = 0.13). In contrast, we observed significant difference in overall survival when these same samples were analyzed according to their gene expression groupings (Figure 1d, Logrank test for trend, p = 0.02). Consistent with the preponderance of pancreatic tumors, the patients in.