Detection of a novel panel of 24 genes with high frequencies of mutation in gastric cancer based on next-generation sequencing

doi:10.12998/wjcc.v10.i15.4761

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World Journal of Clinical Cases

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Clinical and Translational Research

World J Clin Cases. May 26, 2022; 10(15): 4761-4775
Published online May 26, 2022. doi: 10.12998/wjcc.v10.i15.4761

Detection of a novel panel of 24 genes with high frequencies of mutation in gastric cancer based on next-generation sequencing

Hui-Hui Zeng, Ze Yang, Ye-Bei Qiu, Shoaib Bashir, Yin Li, Meng Xu

Hui-Hui Zeng, Ye-Bei Qiu, Shoaib Bashir, Yin Li, Meng Xu, Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou 510630, Guangdong Province, China

Hui-Hui Zeng, Department of Medical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, Anhui Province, China

Ze Yang, Department of Oncology, Jinan University, Guangzhou 510630, Guangdong Province, China

Author contributions: Xu M and Li Y conceived and designed this study; Zeng HH, Ze Yang, and Qiu YB were responsible for the data collection and analysis; Bashir S wrote the draft manuscript; Xu M and Li Y revised the manuscript; all authors critically reviewed the manuscript and approved the final manuscript for publication.

Supported by the Science and Technology Foundation of Guangzhou, No. 201803010059, and the Natural Science Foundation of Bengbu Medical College, No. BYKY2019129ZD.

Institutional review board statement: This study was approved by the Medical Ethics Committee of the First Affiliated Hospital of Bengbu Medical College (No. 2021KY029).

Informed consent statement: Informed written consent was obtained from the patient, all patients signed informed consent voluntarily.

Conflict-of-interest statement: The authors declare that they have no competing interests.

Data sharing statement: No additional data are available.

Corresponding author: Meng Xu, MD, PhD, Full Professor, Department of Oncology, The First Affiliated Hospital of Jinan University, No. 613 West Huangpu Avenue, Guangzhou 510630, Guangdong Province, China. 641704010@qq.com

Received: December 16, 2021
Peer-review started: December 16, 2021
First decision: January 27, 2022
Revised: February 6, 2022
Accepted: March 26, 2022
Article in press: March 26, 2022
Published online: May 26, 2022
Processing time: 158 Days and 23.3 Hours

ARTICLE HIGHLIGHTS

Research background

Next-generation sequencing (NGS) technology combined with bioinformatics methods provides quick identification of differences in mutated genes and valuable gene expression information. However, NGS has not been widely used to diagnose and treat gastric cancer in clinical practice.

Research motivation

The Cancer Genome Atlas (TCGA) and the Asian Cancer Research Group (ACRG) have provided unprecedented insight into the molecular characteristics of gastric cancer. We constructed a panel of 24 mutant genes to identify promising target sites.

Research objectives

We used germline DNA from FFPE tumour tissue specimens to explore 24 genes with a high frequency of mutation, including ATR, ATM, AR, BRCA2, BMPR1A, CHD4, CDKN2A, ERBB2, ERBB3, FBXW7, FGFR2, KRAS, KDR, KIT, MET, MSH2, MTOR, NF1, PTEN, PDGFRA, PIK3CA, PTPN11, STK11, and TP53.

Research methods

24 genes with a high frequency of mutation were compared using the cBioPortal database. Then, the clinical annotation of important variant mutation sites was evaluated with the ClinVar database. Finally, candidate drugs for targeted therapy and immunotherapy were identified from the OncoKB database.

Research results

TP53, ERBB2, BRCA2, NF1, and PIK3CA had a higher mutation frequency in our data and the cBioPortal database. MSS was the primary type of MSI. BRCA2, PIK3CA, and FGFR2 gene mutations were identified as promising biomarkers in gastric cancer.

Research conclusions

In the present study, the 24 mutated genes were detected in all 64 patients. This novel panel of 24 genes with high frequencies of mutation might provide new insights for individualized and precise treatment of gastric cancer patients.

Research perspectives

An efficient custom panel of 24 mutant genes can rapidly identify common drug targets with a relatively low detection cost. Furthermore, it can offer effective personalized treatment for gastric cancer patients.