Analyzing the profile of chromosomal imbalances in esophageal atypical hyperplasia and early stage esophageal squamous cell carcinoma by 250K Snp Array

Abstract

To detect DNA copy number abnormality and LOH and explore the profile of chromosomal imbalances in esophageal atypical hyperplasia and early stage esophageal squamous cell carcinoma using SNP array. The DNA copy number abnormality and LOH in pathological change esophageal tissue and matched normal esophageal tissue of one case of primary esophageal high atypical hyperplasia and four cases of primary early stage esophageal squamous cell carcinoma were detected by using Affymetrix GeneChip Human Mapping 250K Nsp Array. Amplification was found in a few DNA fragment and no deletion or LOH was found in esophageal high atypical hyperplasia. In early stage esophageal squamous cell carcinoma, DNA amplification occurred in 1p, 1q, 2p, 2q, 3q, 4q, 5p, 6p, 6q, 7q, 8q, 11p, 11q, 12p, 12q, 14q, 17q, 18p, 19q, 20q, 22q and X chromosome. DNA deletion occurred in 1p, 2q, 3p, 3q, 4p, 4q, 8p, 9p, 9q, 10q, 11p, 13q, 16p, 18q, 19p, 19q and 22q chromosome. LOH occurred in 3q and 9q chromosome. The amplification in 1p, 19q, 4q, 11p chromosome and the deletion in 3q, 11p, 2q, 16p chromosome were rarely reported. DNA abnormality was rare in esophageal high atypical hyperplasia. The obvious amplification and deletion in DNA have been found in early stage esophageal squamous cell carcinoma, but LOH was rarely found. 250K SNP array could effectively detect DNA copy number change and LOH in whole-wide genes in esophageal atypical hyperplasia and early stage esophageal squamous cell carcinoma with high distinguishability and precise location. The results would provide important academic information for detection and location of related genes in early stage esophageal squamous cell carcinoma.