Basic Study
Copyright ©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastrointest Oncol. Mar 15, 2022; 14(3): 690-702
Published online Mar 15, 2022. doi: 10.4251/wjgo.v14.i3.690
Cost-effective low-coverage whole-genome sequencing assay for the risk stratification of gastric cancer
Li-Ping Ye, Xin-Li Mao, Xian-Bin Zhou, Yi Wang, Shi-Wen Xu, Sai-Qin He, Zi-Liang Qian, Xiao-Gang Zhang, Li-Juan Zhai, Jin-Bang Peng, Bin-Bin Gu, Xiu-Xiu Jin, Ya-Qi Song, Shao-Wei Li
Li-Ping Ye, Xin-Li Mao, Xian-Bin Zhou, Yi Wang, Sai-Qin He, Jin-Bang Peng, Bin-Bin Gu, Xiu-Xiu Jin, Shao-Wei Li, Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
Li-Ping Ye, Xin-Li Mao, Xian-Bin Zhou, Yi Wang, Sai-Qin He, Jin-Bang Peng, Bin-Bin Gu, Xiu-Xiu Jin, Shao-Wei Li, Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
Li-Ping Ye, Xin-Li Mao, Xian-Bin Zhou, Yi Wang, Sai-Qin He, Jin-Bang Peng, Bin-Bin Gu, Xiu-Xiu Jin, Shao-Wei Li, Institute of Digestive Disease, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
Shi-Wen Xu, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai 317000, Zhejiang Province, China
Zi-Liang Qian, Suzhou Hongyuan Biotech Inc., Suzhou 215000, Zhejiang Province, China
Zi-Liang Qian, Prophet Genomics Inc., California, CA 95101, United States
Xiao-Gang Zhang, Catcher Bio Inc., Hangzhou 310000, Zhejiang Province, China
Li-Juan Zhai, Department of Medicine, Catcher Bio Inc., Hangzhou 310000, Zhejiang Province, China
Ya-Qi Song, Taizhou Hospital of Zhejiang Province, Zhejiang University School of Medicine, Linhai 317000, Zhejiang Province, China
Author contributions: Zhou XB, Wang Y, He SQ, Zhang XG, Zhai LJ, Peng JB, Gu BB, Jin XX, Song YQ, and Ye LP participated in the design of the study and performed the statistical analysis; Mao XL, Xu SW, Qian ZL, and Li SW drafted the manuscript. All authors read and approved the final manuscript.
Supported by Program of Taizhou Science and Technology Grant, No. 20ywb29; Medical Health Science and Technology Project of Zhejiang Province, No. 2021PY083; Key Technology Research and Development Program of Zhejiang Province, No. 2019C03040; Open Project Program of Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, No. 21SZDSYS01 and 21SZDSYS09; and Major Research Program of Taizhou Enze Medical Center Grant, No. 19EZZDA2.
Institutional review board statement: The study was reviewed and approved by the the Institutional Ethics Committee of Taizhou Hospital of Zhejiang Province (Approval No. K20201205).
Conflict-of-interest statement: Author Qian ZL was employed by the company Suzhou Hongyuan Biotech Inc., and Zhang XG and Zhai LJ were employed by the company Catcher Bio Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Data sharing statement: Technical appendix, statistical code, and dataset available from the corresponding author at li_shaowei81@hotmai.com.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/
Corresponding author: Shao-Wei Li, PhD, Academic Fellow, Assistant Professor, Associate Research Scientist, Instructor, Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, No. 150 Xinmen Street, Linhai 317000, Zhejiang Province, China. li_shaowei81@hotmail.com
Received: August 10, 2021
Peer-review started: August 10, 2021
First decision: December 4, 2021
Revised: December 25, 2021
Accepted: February 22, 2022
Article in press: February 22, 2022
Published online: March 15, 2022
ARTICLE HIGHLIGHTS
Research background

These findings from our research may be instructive for future research on the treatment and prevention of gastric cancer (GC).

Research motivation

Thus, using low-coverage whole-genome sequencing, GC can be classified into three categories based on disease etiology; this classification may prove useful for GC diagnosis and precision medicine.

Research objectives

Epstein-Barr virus (EBV) enrichment was found to be associated with tumors in the gastric cardia and fundus. Helicobacter pylori (H. pylori) enrichment was found to be associated with tumors in the pylorus and antrum.

Research methods

DNA from the 40 GC patients were subjected to low-coverage whole-genome sequencing by Illumina × 10, followed by copy number analyses using a customized bioinformatics workflow ultrasensitive chromosomal aneuploidy detector. EBV-positive tumors had the best prognosis, whereas patients with higher genomic instability showed the worst survival.

Research results

To investigate biomarkers for GC sub-typing by cost-effective, low-coverage whole-genome sequencing.

Research conclusions

To search for new biomarkers of GC subtypes.

Research perspectives

GC, a multifactorial disease, is caused by pathogens like H. pylori or EBV and by genetic components.