J Korean Med Sci.  2023 Aug;38(32):e255. 10.3346/jkms.2023.38.e255.

Sample Collection Methods in Upper Gastrointestinal Research

  • 1Division of Gastroenterology, Department of Internal Medicine and Gastrointestinal Cancer Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
  • 2Division of Gastroenterology, Department of Internal Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
  • 3Department of Internal Medicine, Inje University College of Medicine, Haeundae Paik Hospital, Busan, Korea
  • 4Division of Gastroenterology, Department of Internal Medicine, Yongin Severance Hospital, Yonsei University College of Medicine, Yongin, Korea
  • 5Division of Gastroenterology, Department of Internal Medicine, College of Medicine, Incheon St. Mary’s Hospital, The Catholic University of Korea, Incheon, Korea
  • 6Division of Gastroenterology, Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
  • 7Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
  • 8Department of Food Science and Biotechnology, Sejong University, Seoul, Korea
  • 9Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
  • 10Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea


In recent years, significant translational research advances have been made in the upper gastrointestinal (GI) research field. Endoscopic evaluation is a reasonable option for acquiring upper GI tissue for research purposes because it has minimal risk and can be applied to unresectable gastric cancer. The optimal number of biopsy samples and sample storage is crucial and might influence results. Furthermore, the methods for sample acquisition can be applied differently according to the research purpose; however, there have been few reports on methods for sample collection from endoscopic biopsies. In this review, we suggested a protocol for collecting study samples for upper GI research, including microbiome, DNA, RNA, protein, single-cell RNA sequencing, and organoid culture, through a comprehensive literature review. For microbiome analysis, one or two pieces of biopsied material obtained using standard endoscopic forceps may be sufficient. Additionally, 5 mL of gastric fluid and 3–4 mL of saliva is recommended for microbiome analyses. At least one gastric biopsy tissue is necessary for most DNA or RNA analyses, while proteomics analysis may require at least 2–3 biopsy tissues. Single cell-RNA sequencing requires at least 3–5 tissues and additional 1–2 tissues, if possible. For successful organoid culture, multiple sampling is necessary to improve the quality of specimens.


Endoscopy; Biopsy; Translational Research; Sample


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