Pangenomic analysis of Chinese gastric cancer

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-...

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Autores principales: Yu, Yingyan, Zhang, Zhen, Dong, Xiaorui, Yang, Ruixin, Duan, Zhongqu, Xiang, Zhen, Li, Jun, Li, Guichao, Yan, Fazhe, Xue, Hongzhang, Jiao, Du, Lu, Jinyuan, Lu, Huimin, Zhang, Wenmin, Wei, Yangzhen, Fan, Shiyu, Li, Jing, Jia, Jingya, Zhang, Jun, Ji, Jun, Liu, Pixu, Lu, Hui, Zhao, Hongyu, Chen, Saijuan, Wei, Chaochun, Chen, Hongzhuan, Zhu, Zhenggang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477819/
https://www.ncbi.nlm.nih.gov/pubmed/36109518
http://dx.doi.org/10.1038/s41467-022-33073-7
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author Yu, Yingyan
Zhang, Zhen
Dong, Xiaorui
Yang, Ruixin
Duan, Zhongqu
Xiang, Zhen
Li, Jun
Li, Guichao
Yan, Fazhe
Xue, Hongzhang
Jiao, Du
Lu, Jinyuan
Lu, Huimin
Zhang, Wenmin
Wei, Yangzhen
Fan, Shiyu
Li, Jing
Jia, Jingya
Zhang, Jun
Ji, Jun
Liu, Pixu
Lu, Hui
Zhao, Hongyu
Chen, Saijuan
Wei, Chaochun
Chen, Hongzhuan
Zhu, Zhenggang
author_facet Yu, Yingyan
Zhang, Zhen
Dong, Xiaorui
Yang, Ruixin
Duan, Zhongqu
Xiang, Zhen
Li, Jun
Li, Guichao
Yan, Fazhe
Xue, Hongzhang
Jiao, Du
Lu, Jinyuan
Lu, Huimin
Zhang, Wenmin
Wei, Yangzhen
Fan, Shiyu
Li, Jing
Jia, Jingya
Zhang, Jun
Ji, Jun
Liu, Pixu
Lu, Hui
Zhao, Hongyu
Chen, Saijuan
Wei, Chaochun
Chen, Hongzhuan
Zhu, Zhenggang
author_sort Yu, Yingyan
collection PubMed
description 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.
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spelling pubmed-94778192022-09-17 Pangenomic analysis of Chinese gastric cancer Yu, Yingyan Zhang, Zhen Dong, Xiaorui Yang, Ruixin Duan, Zhongqu Xiang, Zhen Li, Jun Li, Guichao Yan, Fazhe Xue, Hongzhang Jiao, Du Lu, Jinyuan Lu, Huimin Zhang, Wenmin Wei, Yangzhen Fan, Shiyu Li, Jing Jia, Jingya Zhang, Jun Ji, Jun Liu, Pixu Lu, Hui Zhao, Hongyu Chen, Saijuan Wei, Chaochun Chen, Hongzhuan Zhu, Zhenggang Nat Commun Article 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. Nature Publishing Group UK 2022-09-15 /pmc/articles/PMC9477819/ /pubmed/36109518 http://dx.doi.org/10.1038/s41467-022-33073-7 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Yu, Yingyan
Zhang, Zhen
Dong, Xiaorui
Yang, Ruixin
Duan, Zhongqu
Xiang, Zhen
Li, Jun
Li, Guichao
Yan, Fazhe
Xue, Hongzhang
Jiao, Du
Lu, Jinyuan
Lu, Huimin
Zhang, Wenmin
Wei, Yangzhen
Fan, Shiyu
Li, Jing
Jia, Jingya
Zhang, Jun
Ji, Jun
Liu, Pixu
Lu, Hui
Zhao, Hongyu
Chen, Saijuan
Wei, Chaochun
Chen, Hongzhuan
Zhu, Zhenggang
Pangenomic analysis of Chinese gastric cancer
title Pangenomic analysis of Chinese gastric cancer
title_full Pangenomic analysis of Chinese gastric cancer
title_fullStr Pangenomic analysis of Chinese gastric cancer
title_full_unstemmed Pangenomic analysis of Chinese gastric cancer
title_short Pangenomic analysis of Chinese gastric cancer
title_sort pangenomic analysis of chinese gastric cancer
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477819/
https://www.ncbi.nlm.nih.gov/pubmed/36109518
http://dx.doi.org/10.1038/s41467-022-33073-7
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