Concordance between somatic copy number loss and downregulated expression: A pan-cancer study of cancer predisposition genes

Ran Wei; Ming Zhao; Chun-Hou Zheng; Min Zhao; Junfeng Xia

doi:10.1038/srep37358

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Concordance between somatic copy number loss and downregulated expression: A pan-cancer study of cancer predisposition genes

Journal article

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Concordance between somatic copy number loss and downregulated expression: A pan-cancer study of cancer predisposition genes

Ran Wei, Ming Zhao, Chun-Hou Zheng, Min Zhao and Junfeng Xia

Scientific Reports, Vol.6(37358)

2016

DOI: https://doi.org/10.1038/srep37358

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Abstract

Cancer predisposition genes (CPGs) are a class of cancer genes in which germline variants lead to increased risk of cancer. Research has revealed that copy number variation (CNV) may be linked to cancer susceptibility in CPGs. In this pan-cancer analysis, we explored the relationship between somatic CNV and gene expression changes in CPGs. Based on curated 827 human CPGs from literature, we firstly identified 729 CPGs with precise CNV information from 5067 tumor samples using TCGA CNV data. Among them, 128 CPGs tended to have more frequent copy number losses (CNLs) compared with copy number gains (CNGs). Then by correlating these CNV data with TCGA gene expression data, we obtained 49 CPGs with concordant CNLs and gene down-regulation. Intriguingly, five CPGs showed concordance between CNL and down-regulation in 50 or more tumor samples: MTAP (216 samples), PTEN (143), MCPH1 (86), SMAD4 (63), and MINPP1 (51), which may represent the recurrent driving force for gene expression change during oncogenesis. Moreover, network analysis revealed that these 49 CPGs were tightly connected. In summary, this study provides the first observation of concordance etween CNLs and down-regulation of CPGs in pan-cancer, which may help better understand the CPG biology in tumorigenesis and cancer progression.

Details

Title: Concordance between somatic copy number loss and downregulated expression: A pan-cancer study of cancer predisposition genes
Authors: Ran Wei (Author) - Anhui University, China
Ming Zhao (Author) - Anhui University, China
Chun-Hou Zheng (Author) - Anhui University, China
Min Zhao (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Junfeng Xia (Author) - Anhui University, China
Publication details: Scientific Reports, Vol.6(37358); 9
Publisher: Nature Publishing Group
Date published: 2016
DOI: 10.1038/srep37358
ISSN: 2045-2322
Copyright note: Copyright © 2016 The Author. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99451303502621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Oncology

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