Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium

Abstract We begin by arguing that the often used algorithm for the discovery and use of disease risk factors, stepwise logistic regression, is unstable. We then argue that there are other algorithms available that are much more stable and reliable (e.g. the lasso and gradient boosting). We then prop...

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Autores principales:	David E. Booth, Venugopal Gopalakrishna-Remani, Matthew L. Cooper, Fiona R. Green, Margaret P. Rayman
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7ba5a9efd9e749778f882d2f6860e03c
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spelling	oai:doaj.org-article:7ba5a9efd9e749778f882d2f6860e03c2021-12-02T19:12:27ZBoosting and lassoing new prostate cancer SNP risk factors and their connection to selenium10.1038/s41598-021-97412-22045-2322https://doaj.org/article/7ba5a9efd9e749778f882d2f6860e03c2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97412-2https://doaj.org/toc/2045-2322Abstract We begin by arguing that the often used algorithm for the discovery and use of disease risk factors, stepwise logistic regression, is unstable. We then argue that there are other algorithms available that are much more stable and reliable (e.g. the lasso and gradient boosting). We then propose a protocol for the discovery and use of risk factors using lasso or boosting variable selection. We then illustrate the use of the protocol with a set of prostate cancer data and show that it recovers known risk factors. Finally, we use the protocol to identify new and important SNP based risk factors for prostate cancer and further seek evidence for or against the hypothesis of an anticancer function for Selenium in prostate cancer. We find that the anticancer effect may depend on the SNP-SNP interaction and, in particular, which alleles are present.David E. BoothVenugopal Gopalakrishna-RemaniMatthew L. CooperFiona R. GreenMargaret P. RaymanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q David E. Booth Venugopal Gopalakrishna-Remani Matthew L. Cooper Fiona R. Green Margaret P. Rayman Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium
description	Abstract We begin by arguing that the often used algorithm for the discovery and use of disease risk factors, stepwise logistic regression, is unstable. We then argue that there are other algorithms available that are much more stable and reliable (e.g. the lasso and gradient boosting). We then propose a protocol for the discovery and use of risk factors using lasso or boosting variable selection. We then illustrate the use of the protocol with a set of prostate cancer data and show that it recovers known risk factors. Finally, we use the protocol to identify new and important SNP based risk factors for prostate cancer and further seek evidence for or against the hypothesis of an anticancer function for Selenium in prostate cancer. We find that the anticancer effect may depend on the SNP-SNP interaction and, in particular, which alleles are present.
format	article
author	David E. Booth Venugopal Gopalakrishna-Remani Matthew L. Cooper Fiona R. Green Margaret P. Rayman
author_facet	David E. Booth Venugopal Gopalakrishna-Remani Matthew L. Cooper Fiona R. Green Margaret P. Rayman
author_sort	David E. Booth
title	Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium
title_short	Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium
title_full	Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium
title_fullStr	Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium
title_full_unstemmed	Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium
title_sort	boosting and lassoing new prostate cancer snp risk factors and their connection to selenium
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/7ba5a9efd9e749778f882d2f6860e03c
work_keys_str_mv	AT davidebooth boostingandlassoingnewprostatecancersnpriskfactorsandtheirconnectiontoselenium AT venugopalgopalakrishnaremani boostingandlassoingnewprostatecancersnpriskfactorsandtheirconnectiontoselenium AT matthewlcooper boostingandlassoingnewprostatecancersnpriskfactorsandtheirconnectiontoselenium AT fionargreen boostingandlassoingnewprostatecancersnpriskfactorsandtheirconnectiontoselenium AT margaretprayman boostingandlassoingnewprostatecancersnpriskfactorsandtheirconnectiontoselenium
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Boosting and lassoing new prostate cancer SNP risk factors and their connection to selenium

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