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SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival
Genome-wide association studies (GWASs) underlying case-control design have uncovered hundreds of genetic loci involved in tumorigenesis and provided rich resources for identifying risk factors and biomarkers associated with cancer susceptibility. However, the application of GWAS in determining the...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825440/ https://www.ncbi.nlm.nih.gov/pubmed/35947748 http://dx.doi.org/10.1093/nar/gkac677 |
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author | Xin, Junyi Gu, Dongying Chen, Silu Ben, Shuai Li, Huiqin Zhang, Zhengdong Du, Mulong Wang, Meilin |
author_facet | Xin, Junyi Gu, Dongying Chen, Silu Ben, Shuai Li, Huiqin Zhang, Zhengdong Du, Mulong Wang, Meilin |
author_sort | Xin, Junyi |
collection | PubMed |
description | Genome-wide association studies (GWASs) underlying case-control design have uncovered hundreds of genetic loci involved in tumorigenesis and provided rich resources for identifying risk factors and biomarkers associated with cancer susceptibility. However, the application of GWAS in determining the genetic architecture of cancer survival remains unestablished. Here, we systematically evaluated genetic effects at the genome-wide level on cancer survival that included overall survival (OS) and cancer-specific survival (CSS), leveraging data deposited in the UK Biobank cohort of a total of 19 628 incident patients across 17 cancer types. Furthermore, we assessed the causal effects of risk factors and circulating biomarkers on cancer prognosis via a Mendelian randomization (MR) analytic framework, which integrated cancer survival GWAS dataset, along with phenome-wide association study (PheWAS) and blood genome-wide gene expression/DNA methylation quantitative trait loci (eQTL/meQTL) datasets. On average, more than 10 traits, 700 genes, and 4,500 CpG sites were prone to cancer prognosis. Finally, we developed a user-friendly online database, SUrvival related cancer Multi-omics database via MEndelian Randomization (SUMMER; http://njmu-edu.cn:3838/SUMMER/), to help users query, browse, and download cancer survival results. In conclusion, SUMMER provides an important resource to assist the research community in understanding the genetic mechanisms of cancer survival. |
format | Online Article Text |
id | pubmed-9825440 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98254402023-01-10 SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival Xin, Junyi Gu, Dongying Chen, Silu Ben, Shuai Li, Huiqin Zhang, Zhengdong Du, Mulong Wang, Meilin Nucleic Acids Res Database Issue Genome-wide association studies (GWASs) underlying case-control design have uncovered hundreds of genetic loci involved in tumorigenesis and provided rich resources for identifying risk factors and biomarkers associated with cancer susceptibility. However, the application of GWAS in determining the genetic architecture of cancer survival remains unestablished. Here, we systematically evaluated genetic effects at the genome-wide level on cancer survival that included overall survival (OS) and cancer-specific survival (CSS), leveraging data deposited in the UK Biobank cohort of a total of 19 628 incident patients across 17 cancer types. Furthermore, we assessed the causal effects of risk factors and circulating biomarkers on cancer prognosis via a Mendelian randomization (MR) analytic framework, which integrated cancer survival GWAS dataset, along with phenome-wide association study (PheWAS) and blood genome-wide gene expression/DNA methylation quantitative trait loci (eQTL/meQTL) datasets. On average, more than 10 traits, 700 genes, and 4,500 CpG sites were prone to cancer prognosis. Finally, we developed a user-friendly online database, SUrvival related cancer Multi-omics database via MEndelian Randomization (SUMMER; http://njmu-edu.cn:3838/SUMMER/), to help users query, browse, and download cancer survival results. In conclusion, SUMMER provides an important resource to assist the research community in understanding the genetic mechanisms of cancer survival. Oxford University Press 2022-08-10 /pmc/articles/PMC9825440/ /pubmed/35947748 http://dx.doi.org/10.1093/nar/gkac677 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Xin, Junyi Gu, Dongying Chen, Silu Ben, Shuai Li, Huiqin Zhang, Zhengdong Du, Mulong Wang, Meilin SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival |
title | SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival |
title_full | SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival |
title_fullStr | SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival |
title_full_unstemmed | SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival |
title_short | SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival |
title_sort | summer: a mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825440/ https://www.ncbi.nlm.nih.gov/pubmed/35947748 http://dx.doi.org/10.1093/nar/gkac677 |
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