Pharmacogenomic Study of Docetaxel and Cisplatin, Followed by Docetaxel, Cisplatin and Irradiation.

Inclusion Criteria: * Patients must have histological or cytological confirmed esophageal adenocarcinoma or adenocarcinoma of the gastroesophageal junction (this diagnosis will be rendered by the gastroenterology endoscopist, and refers to tumors at the junction of the esophagus and the stomach, where \>50% of the tumor mass is above the diaphragm). Tumors must not have greater than 2cm extension into the the cardia. * Stage T2N0M0, T3N0M0, T1-3N1M0, T1-3N0-1M1a as determined by imaging studies and endoscopic ultrasound staging. M1a disease (celiac nodal metastasis) is permitted if other eligibility criteria are met. Any lesion suspicious for metastasis should biopsied (either by tru cut or fine needle aspiration) to prove eligibility. * The subject has been deemed an appropriate surgical candidate by one of the surgical subinvestigators (ie. Not T4). * No medical comorbidity making the patient not a surgical candidate. * Subject must be 18 years or older * Subject must understand the consent and be willing to give written and informed consent to participate in this investigational protocol, and for a tumor biopsy to be performed for research purposes at the time of their staging endoscopic ultrasound (clinically required for their care), and for a portion of their resection specimen be subjected to experimental laboratory analysis * ECOG performance status \<1 (Karnofsky \>80%; see Appendix A). * Subjects must have adequate caloric intake, as determined by a nutrition evaluation by a registered dietician. Nutrition intake may be enteral, hyperalimentation by enteral feeding tube, or by parenteral nutrition. * Patients must have normal organ and marrow function as defined as: leukocytes \>3,000/mcL; absolute neutrophil count \>1,500/mcL; platelets \>100,000/mcL; hemoglobin \> 8 g/dl; Creatinine clearance (estimated by Cockroft-Gault equation) \>50-mL/min/1.73 m2 for patients with creatinine levels above institutional normal * Hepatic: Total bilirubin must be \< ULN; AST and ALT and alkaline phosphatase must both be less than 2.5 x ULN. * Has a negative serum or urine pregnancy test within 7 days prior to initiation of therapy (female patients of childbearing potential). Exclusion Criteria: * Patients may not be receiving any other investigational agents. * Common Toxicity Criteria Adverse Events version 3 (CTCAEv3) greater than grade 1 peripheral neuropathy. * Uncontrolled intercurrent illness including, but not limited to, ongoing or active infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social situations that would limit compliance with study requirements. Clinically significant cardiac disease (e.g. congestive heart failure, symptomatic coronary artery disease and cardiac arrhythmias not well controlled with medication) or myocardial infarction within the last 12 months. * Pregnant and nursing women are excluded from this study. Women / men of childbearing potential not using a reliable and appropriate contraceptive method. Woman of childbearing potential with either a positive or no pregnancy test at baseline. (Postmenopausal woman must have been amenorrheic for at least 12 months to be considered of non-childbearing potential). Patients will agree to continue contraception for 30 days from the date of the last study drug administration * Patients with a history of severe hypersensitivity reaction to docetaxel, cisplatin, or drugs formulated with polysorbate (Tween) 80. * Because patients with immune deficiency are at increased risk of lethal infections when treated with marrow-suppressive therapy, HIV-positive patients receiving combination anti-retroviral therapy are excluded from the study because of possible pharmacokinetic interactions with cisplatin and docetaxel or other agents administered during the study. * Major surgery within 4 weeks of the start of study treatment, without complete recovery. * History of clinically significant interstitial lung disease and/or pulmonary fibrosis. * Treatment for other carcinomas within the last five years, except cured non-melanoma skin and treated in-situ cervical cancer. * Clinical or radiographic evidence of a tracheobronchial fistula or invasion of the aorta (i.e. T4 disease).