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Cost-effective low-coverage whole-genome sequencing assay for the risk stratification of gastric cancer

World Journal of Gastrointestinal Oncology 2022年第3期14卷 690-702页

作者： 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 Key Laboratory of Minimally Invasive Techniques&Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical UniversityLinhai 317000Zhejiang ProvinceChina Department of Gastroenterology Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical UniversityLinhai 317000Zhejiang ProvinceChina Institute of Digestive Disease Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical UniversityLinhai 317000Zhejiang ProvinceChina Taizhou Hospital of Zhejiang Province Wenzhou Medical UniversityLinhai 317000Zhejiang ProvinceChina Suzhou Hongyuan Biotech Inc. Suzhou 215000Zhejiang ProvinceChina Prophet Genomics Inc. CaliforniaCA 95101United States Catcher Bio Inc. Hangzhou 310000Zhejiang ProvinceChina Department of Medicine Catcher Bio Inc.Hangzhou 310000Zhejiang ProvinceChina Taizhou Hospital of Zhejiang Province Zhejiang University School of MedicineLinhai 317000Zhejiang ProvinceChina

BACKGROUND Gastric cancer(GC), a multifactorial disease, is caused by pathogens, such as helicobacter pylori(H. pylori) and Epstein-Barr virus(EBV), and genetic *** To investigate microbiomes and host genome instability by cost-effective,low-coverage wholegenome sequencing,as biomarkers for GC *** Samples from 40 GC patients were collected from Taizhou Hospital,Zhejiang Province,affiliated with Wenzhou Medical *** from the samples was subjected to low-coverage wholegenome sequencing with a median genome coverage of 1.86×(range:1.03×to 3.17×) by Illumina×10,followed by copy number analyses using a customized bioinformatics workflow ultrasensitive chromosomal aneuploidy *** Of the 40 GC samples,20 (50%) were found to be enriched with *** DNA was detected in 5 GC patients (12.5%).*** DNA was found in 15 (37.5%) *** other 20(50%) patients were found to have relatively higher genomic *** number amplifications of the oncogenes,ERBB2 and KRAS,were found in 9 (22.5%) and 7 (17.5%) of the GC samples,*** enrichment was found to be associated with tumors in the gastric cardia and *** enrichment was found to be associated with tumors in the pylorus and *** with elevated genomic instability showed no localization and could be observed in any ***,***-enriched GC was found to be associated with the Borrmann type Ⅱ/Ⅲ and gastritis ***-enriched GC was not associated with *** statistically significant correlation was observed between genomic instability and ***,these three different molecular subtypes showed distinct survival outcomes (P=0.019).EBV-positive tumors had the best prognosis,whereas patients with high genomic instability (CIN+) showed the worst *** with *** infection showed intermediate prognosis compared with the other two *** Thus,using low-coverage whole-ge

关键词： Gastric cancer Whole-genome sequencing helicobacter pylori infections Epstein-Barr virus infections Genetic components Precision medicine

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