amplifying DNA complementary to the microsatellite regions of 1q22, 1p34.2, 1p22.3, 1p36.21, 1p36.21, B Catenin E3, 3p25, 3p12.3, 3p22.3, 3p24.3, 3p26.3, 3p11.2, 3p24.2, C-KIT Ell, C-KIT E17, 5q23.1, 5q23.2, BRAF E15, EGFR E 19, EGFR E 21, 7p12.3, 7p12.1, 9p21.1, 9p23, 10q23.32, 10q23.33, HRAS1 E1, Kras2.E1, Kras2.E2, 17q22, 17q21.2, 17q11.2, 17p13.1 17p13, 17p13.1, 18q21.33, 19q13.2, 19q13.32, 21q21.2, 22q13.2, and Xp22.2 from a subject;

detecting the presence or absence of a mutation in the microsatellite regions;

categorizing clonality of each mutation;

calculating a mutational load based on the sum of low and high clonality mutations;

comparing the mutational load with a series of pre-determined mutational load cut-offs defining risk categories;

assigning the subject to a risk category corresponding to the subject's mutational load, wherein each risk category is indicative of the risk of disease progression;

determining if the subject is in a high risk category for disease progression from Barrett's metaplasia to esophageal adenocarcinoma; and

administering to the subject identified in the high risk category at least one treatment modality selected from endoscopic mucosal resection, endoscopic submucosal dissection, a therapeutically effective amount of radiofrequency ablation, a therapeutically effective amount of cryoablation, a therapeutically effective amount of photodynamic therapy and combinations thereof.