Comprehensive Esophageal Cancer Gene Panel

The in-house panel was designed by referring to the previous studies with Ion AmpliSeq designer software (Thermo Fisher Scientific)^{24 (link),25 (link)}. Sixty-nine significantly mutated genes (SMGs) were included to cover SMGs for both EAC and esophageal squamous cell carcinoma (Fig. 2). The SMGs were selected according to (1) genes that are often involved in esophageal cancer (EC), obtained from TCGA and other projects^{9 (link),10 (link),26 (link)–28 (link)} and (2) genes frequently mutated in EC, referring to the COSMIC database (http://cancer.sanger.ac.uk/cancergenome/projects/cosmic). Finally, the panel consisted of 4410 primer pairs.Figure 2

List of 69 significant mutated genes included in the panel. Each box shows each gene included in the panel.

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Tokunaga M., Okimoto K., Akizue N., Ishikawa K., Hirotsu Y., Amemiya K., Ota M., Matsusaka K., Nishimura M., Matsushita K., Ishikawa T., Nagashima A., Shiratori W., Kaneko T., Oura H., Kanayama K., Ohta Y., Taida T., Saito K., Matsumura T., Chiba T., Mochizuki H., Arai M., Kato J., Ikeda J.I., Omata M, & Kato N. (2021). Genetic profiles of Barrett’s esophagus and esophageal adenocarcinoma in Japanese patients. Scientific Reports, 11, 17671.

Publication 2021

Ion AmpliSeq designer software

Cancer Cosmic Esophageal cancer Esophageal squamous cell carcinoma Gene Primer

Corresponding Organization :

Other organizations : Chiba University, Yamanashi Prefectural Central Hospital, Chiba University Hospital, The University of Tokyo

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Variable analysis

independent variables

The in-house panel was designed by referring to the previous studies with Ion AmpliSeq designer software (Thermo Fisher Scientific)

dependent variables

Sixty-nine significantly mutated genes (SMGs) were included to cover SMGs for both EAC and esophageal squamous cell carcinoma

control variables

Control variables not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned

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