Pangenomic analysis of Chinese gastric cancer

Author:

Yu YingyanORCID,Zhang ZhenORCID,Dong Xiaorui,Yang Ruixin,Duan ZhongquORCID,Xiang Zhen,Li Jun,Li Guichao,Yan Fazhe,Xue HongzhangORCID,Jiao Du,Lu Jinyuan,Lu Huimin,Zhang Wenmin,Wei Yangzhen,Fan Shiyu,Li JingORCID,Jia Jingya,Zhang Jun,Ji Jun,Liu Pixu,Lu HuiORCID,Zhao HongyuORCID,Chen SaijuanORCID,Wei ChaochunORCID,Chen HongzhuanORCID,Zhu ZhenggangORCID

Abstract

AbstractPangenomic 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.

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary

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