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Elsevier"},{"key":"ref9","first-page":"622","article-title":"Squamous Cell Cancers: A Unified Perspective on Biology and Genetics. Cancer Cell","volume":"29","author":"GP Dotto","year":"2016","journal-title":"Elsevier"},{"key":"ref10","unstructured":"Howlader N, Noone AM, Krapcho M, Miller D, Bishop K, Altekruse SF, Kosary CL, Yu M, Ruhl J, Tatalovich Z, Mariotto A, Lewis DR, Chen HS, Feuer EJ CK. SEER Cancer Statistics Review, 1975\u20132013 [Internet]. Bethesda; 2015. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/seer.cancer.gov\/csr\/1975_2013\/sections.html\" xlink:type=\"simple\">https:\/\/seer.cancer.gov\/csr\/1975_2013\/sections.html<\/ext-link>"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2499","DOI":"10.1056\/NEJMra1314530","article-title":"Esophageal Carcinoma","volume":"371","author":"AK Rustgi","year":"2014","journal-title":"N Engl J Med"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2521","DOI":"10.1242\/dev.003855","article-title":"Multiple dose-dependent roles for Sox2 in the patterning and differentiation of anterior foregut endoderm","volume":"134","author":"J Que","year":"2007","journal-title":"Development"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1038\/ng.465","article-title":"SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas","volume":"41","author":"AJ 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