Pangenomic analysis of Chinese gastric cancer

Yingyan Yu (), Zhen Zhang, Xiaorui Dong, Ruixin Yang, Zhongqu Duan, Zhen Xiang, Jun Li, Guichao Li, Fazhe Yan, Hongzhang Xue, Du Jiao, Jinyuan Lu, Huimin Lu, Wenmin Zhang, Yangzhen Wei, Shiyu Fan, Jing Li, Jingya Jia, Jun Zhang, Jun Ji, Pixu Liu, Hui Lu, Hongyu Zhao, Saijuan Chen, Chaochun Wei (), Hongzhuan Chen () and Zhenggang Zhu ()
Additional contact information
Yingyan Yu: Shanghai Jiao Tong University School of Medicine
Zhen Zhang: Fudan University Shanghai Cancer Center
Xiaorui Dong: Shanghai Jiao Tong University
Ruixin Yang: Shanghai Jiao Tong University School of Medicine
Zhongqu Duan: Shanghai Jiao Tong University
Zhen Xiang: Shanghai Jiao Tong University School of Medicine
Jun Li: Shanghai Jiao Tong University School of Medicine
Guichao Li: Fudan University Shanghai Cancer Center
Fazhe Yan: Shanghai Jiao Tong University
Hongzhang Xue: Shanghai Jiao Tong University
Du Jiao: Shanghai Jiao Tong University
Jinyuan Lu: Shanghai Jiao Tong University
Huimin Lu: Shanghai Jiao Tong University
Wenmin Zhang: Shanghai Jiao Tong University
Yangzhen Wei: Shanghai Jiao Tong University
Shiyu Fan: Shanghai Jiao Tong University
Jing Li: Shanghai Jiao Tong University
Jingya Jia: Shanghai Jiao Tong University
Jun Zhang: Shanghai Jiao Tong University School of Medicine
Jun Ji: Shanghai Jiao Tong University School of Medicine
Pixu Liu: Dalian Medical University
Hui Lu: Shanghai Jiao Tong University
Hongyu Zhao: Shanghai Jiao Tong University
Saijuan Chen: Shanghai Jiao Tong University
Chaochun Wei: Shanghai Jiao Tong University
Hongzhuan Chen: Shanghai Jiao Tong University School of Medicine
Zhenggang Zhu: Shanghai Jiao Tong University School of Medicine

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: Abstract Pangenomic study might improve the completeness of human reference genome (GRCh38) and promote precision medicine. Here, we use an automated pipeline of human pangenomic analysis to build gastric cancer pan-genome for 185 paired deep sequencing data (370 samples), and characterize the gene presence-absence variations (PAVs) at whole genome level. Genes ACOT1, GSTM1, SIGLEC14 and UGT2B17 are identified as highly absent genes in gastric cancer population. A set of genes from unaligned sequences with GRCh38 are predicted. We successfully locate one of predicted genes GC0643 on chromosome 9q34.2. Overexpression of GC0643 significantly inhibits cell growth, cell migration and invasion, cell cycle progression, and induces cell apoptosis in cancer cells. The tumor suppressor functions can be reversed by shGC0643 knockdown. The GC0643 is approved by NCBI database (GenBank: MW194843.1). Collectively, the robust pan-genome strategy provides a deeper understanding of the gene PAVs in the human cancer genome.

Date: 2022
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DOI: 10.1038/s41467-022-33073-7

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