Abstract 5133: Copy number variation in 13q32.1 associated with esophageal squamous cell carcinoma

Abstract

Abstract Background: Esophageal squamous cell carcinoma (ESCC) is the major lethal upper gastrointestinal tract cancer in China. The highly regional and family aggregative incidence of ESCC in China suggests that genetic susceptibility contributed to pathogenesis. Copy number variation (CNV) is an important form of gene structure variations and has been associated with multiple complex diseases, such as malignant tumors. This study aimed to identify the common CNVs correlated with ESCC susceptibility and demonstrate the functional significances. Method: A genome-wide associated study was conducted on 128 discordant sibling pairs of ESCC, which were native residents in Yangquan area, Shan Xi Province of China. The genomic DNA of peripheral blood leukocytes were extracted and genotyping was detected using the Illumina HumanHap 610Q BeadChips. After stringent quality control filtering, the CNVs-penotype association analysis were performed using the paired Hidden Markov Model calling algorithm in the Partek Genomic Suite with settings of length above 1kb and minimum 10 consecutive probes. Another 223 Northern Chinese Han people (111 ESCC patients and 112 health controls) were chosen to validate the CNVs using quantitative real-time PCR assays. Then the paraffin-embedded tissue samples of 16 ESCC patients with known genotyping data were collected for immunohistochemistry. Last, the highest frequency of variation region was cloned into luciferase reporter vectors to investigate its biological significance in ESCC cells. Results: A total of 57,774 individual CNVs covering all autosomes were identified. Of them, 13q32.1 was identified as a critical enrichment region, and it mainly was involved in one candidate gene. Conditional logistic regression test showed that this region was significantly associated with ESCC with the odd ratio being 65.289 (95%CI: 11.177-381.366; P<0.001). Quantitative real-time PCR assays replicated CNV in this gene. The frequencies of the three genotypes in cases were 3.6% (1 copy), 74.8% (2 copies), and 21.7% (3 copies), which differed significantly from those in controls (91.1% [2 copies], and 8.9% [3 copies]). Logistic regression analysis showed that the CNV in this gene increased the risk of ESCC (odd ratio: 3.891; 95% CI: 1.53-9.91 P=0.004). Additionally, 9 out of 11 patients containing 3 copies had positive expression of the gene (2 positive and 7 strong positive), whereas only 1 out of 5 patients containing 2 copies had positive expression. Chi-Square analysis showed that there was significant difference between two groups of patients (P=0.018). The subsequently luciferase asaay further comfirmed the enhancer activity of this CNV region. Conclusion: Common CNVs at 13q32.1 was associated with ESCC susceptibility probably due to its potential enhancer activity on regulating the gene expression. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5133. doi:1538-7445.AM2012-5133