Pangenomic analysis of Chinese gastric cancer.
Yingyan YuZhen ZhangXiaorui DongRuixin YangZhongqu DuanZhen XiangJun LiGuichao LiFazhe YanHongzhang XueDu JiaoJinyuan LuHuimin LuWenmin ZhangYangzhen WeiShiyu FanJing LiJingya JiaJun ZhangJun JiPixu LiuHui LuHongyu ZhaoSai-Juan ChenChaochun WeiHong-Zhuan ChenZhenggang ZhuPublished in: Nature communications (2022)
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.
Keyphrases
- genome wide
- genome wide identification
- endothelial cells
- cell cycle
- dna methylation
- cell proliferation
- copy number
- single cell
- genome wide analysis
- pluripotent stem cells
- transcription factor
- stem cells
- bioinformatics analysis
- squamous cell carcinoma
- deep learning
- big data
- machine learning
- young adults
- artificial intelligence
- genetic diversity
- solid phase extraction