We performed genome-wide analysis of copy-number changes and loss of heterozygosity (LOH) in Barrett's esophageal adenocarcinoma by single nucleotide polymorphism (SNP) microarrays to identify associated genomic alterations. DNA from 27 esophageal adenocarcinomas and 14 matching normal tissues was subjected to SNP microarrays. The data were analyzed using dChipSNP software. Copy-number changes occurring in at least 25% of the cases and LOH occurring in at least 19% were regarded as relevant changes. As a validation, fluorescence in situ hybridization (FISH) of 8q24.21 (CMYC) and 8p23.1 (SOX7) was performed. Previously described genomic alterations in esophageal adenocarcinomas could be confirmed by SNP microarrays, such as amplification on 8q (CMYC, confirmed by FISH) and 20q13 or deletion/LOH on 3p (FHIT) and 9p (CDKN2A). Moreover, frequent gains were detected on 2p23.3, 7q11.22, 13q31.1, 14q32.31, 17q23.2 and 20q13.2 harboring several novel candidate genes. The highest copy numbers were seen on 8p23.1, the location of SOX7, which could be demonstrated to be involved in amplification by FISH. A nuclear overexpression of the transcription factor SOX7 could be detected by immunohistochemistry in two amplified tumors. Copy-number losses were seen on 18q21.32 and 20p11.21, harboring interesting candidate genes, such as CDH20 and CST4. Finally, a novel LOH region could be identified on 6p in at least 19% of the cases. In conclusion, SNP microarrays are a valuable tool to detect DNA copynumber changes and LOH at a high resolution. Using this technique, we identified several novel genes and DNA regions associated with esophageal adenocarcinoma. KEYWORDS: Barrett's adenocarcinoma; copy-number changes; esophageal carcinoma; LOH; mapping array; SNP array Genomic alterations, such as amplification, deletion, translocation and loss of heterozygosity (LOH) play an important role in the pathogenesis and progression of cancer due to the activation of oncogenes or inactivation of tumor suppressor genes. Apart from numeric aberrations, such as gene amplification or deletion, which are frequently detected in carcinomas, other genomic changes in carcinogenesis, such as LOH, do not necessarily lead to DNA copy-number gain or loss. Several causes of LOH have been described, including deletion, non-disjunction and reduplication, mitotic recombination and gene conversion. 1 The two-hit model describes a tumor suppressor gene inactivation due to a loss of one allele and mutation of the other allele, resulting in an LOH. 2 Besides detailed investigation of known oncogenes and tumor suppressor genes, screening for novel genomic alterations in different cancers and precursor lesions provides information of molecular mechanisms in carcinogenesis.The incidence of esophageal (Barrett's) adenocarcinoma, mostly arising within the precancerous Barrett's esophagus, with the normal esophageal squamous epithelium changed into intestinal metaplasia, has risen in the past decades in western countries. 3 Screening for chromosomal alterations has bee...