TY - JOUR
T1 - Sample Collection Methods in Upper Gastrointestinal Research
AU - Yang, Hyo Joon
AU - Seo, Seung In
AU - Lee, Jin
AU - Huh, Cheal Wung
AU - Kim, Joon Sung
AU - Park, Jun Chul
AU - Kim, Hyunki
AU - Shin, Hakdong
AU - Shin, Cheol Min
AU - Park, Chan Hyuk
AU - Lee, Sang Kil
N1 - Publisher Copyright:
© 2023 The Korean Academy of Medical Sciences.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - Biopsy
KW - Endoscopy
KW - Sample
KW - Translational Research
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U2 - 10.3346/jkms.2023.38.e255
DO - 10.3346/jkms.2023.38.e255
M3 - Review article
C2 - 37582502
AN - SCOPUS:85168067071
SN - 1011-8934
VL - 38
JO - Journal of Korean medical science
JF - Journal of Korean medical science
IS - 32
M1 - e255
ER -