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Pangenomic analysis of Chinese gastric cancer

Author

Listed:
  • 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
    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
    Shanghai Jiao Tong University)

  • Hongyu Zhao

    (Shanghai Jiao Tong University)

  • Saijuan Chen

    (Shanghai Jiao Tong University)

  • Chaochun Wei

    (Shanghai Jiao Tong University
    Shanghai Jiao Tong University)

  • Hongzhuan Chen

    (Shanghai Jiao Tong University School of Medicine
    Shuguang Hospital, Shanghai University of Traditional Chinese Medicine)

  • Zhenggang Zhu

    (Shanghai Jiao Tong University School of Medicine)

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.

Suggested Citation

  • 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 & Sh, 2022. "Pangenomic analysis of Chinese gastric cancer," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33073-7
    DOI: 10.1038/s41467-022-33073-7
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