Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile

Background: More than 150 types of brain tumors have been documented. Accurate diagnosis is important for making appropriate therapeutic decisions in treating the diseases. The goal of this study is to develop a DNA methylation profile-based classifier to accurately identify various kinds of brain t...

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Autores principales:	Yuxing Chen, Yixin Yan, Moping Xu, Wen Chen, Jinyu Lin, Yan Zhao, Junze Wu, Xianlong Wang
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	machine learning multilayer perceptron model CNS tumors DNA methylation classification Computer applications to medicine. Medical informatics R858-859.7
Acceso en línea:	https://doaj.org/article/0d848c47df394e3783d6250f30cce2ca
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spelling	oai:doaj.org-article:0d848c47df394e3783d6250f30cce2ca2021-11-08T04:42:18ZDevelopment of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile2673-764710.3389/fbinf.2021.744345https://doaj.org/article/0d848c47df394e3783d6250f30cce2ca2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fbinf.2021.744345/fullhttps://doaj.org/toc/2673-7647Background: More than 150 types of brain tumors have been documented. Accurate diagnosis is important for making appropriate therapeutic decisions in treating the diseases. The goal of this study is to develop a DNA methylation profile-based classifier to accurately identify various kinds of brain tumors.Methods: Thirteen datasets of DNA methylation profiles were downloaded from the Gene Expression Omnibus (GEO) database, of which GSE90496 and GSE109379 were used as the training set and the validation set, respectively, and the remaining 11 sets were used as the independent test set. The random forest algorithm was used to select the CpG sites based on the importance of the features and a multilayer perceptron (MLP) model was trained to classify the samples. Deconvolution with the debCAM package was used to explore the cellular composition difference among tumors.Results: From training datasets with 2,801 samples, 396,568 CpG sites were retained after preprocessing, of which 767 were selected as the modeling features. A three-layer MLP model was developed, which consists of 1,320 nodes in the hidden layer, to predict the histological types of brain tumors. The prediction accuracy is 99.2, 87.0, and 96.58%, respectively, on the training, validation and test sets. The results of deconvolution analysis showed that the cell proportions of different tumor subtypes were different, and it is approximately enough to distinguish different tumor entities.Conclusion: We developed a classifier that is robust for the classification of central nervous system tumors, and tried to analyze the reasons for the classification performance.Yuxing ChenYixin YanMoping XuWen ChenJinyu LinYan ZhaoJunze WuXianlong WangXianlong WangFrontiers Media S.A.articlemachine learningmultilayer perceptron modelCNS tumorsDNA methylationclassificationComputer applications to medicine. Medical informaticsR858-859.7ENFrontiers in Bioinformatics, Vol 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	machine learning multilayer perceptron model CNS tumors DNA methylation classification Computer applications to medicine. Medical informatics R858-859.7
spellingShingle	machine learning multilayer perceptron model CNS tumors DNA methylation classification Computer applications to medicine. Medical informatics R858-859.7 Yuxing Chen Yixin Yan Moping Xu Wen Chen Jinyu Lin Yan Zhao Junze Wu Xianlong Wang Xianlong Wang Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile
description	Background: More than 150 types of brain tumors have been documented. Accurate diagnosis is important for making appropriate therapeutic decisions in treating the diseases. The goal of this study is to develop a DNA methylation profile-based classifier to accurately identify various kinds of brain tumors.Methods: Thirteen datasets of DNA methylation profiles were downloaded from the Gene Expression Omnibus (GEO) database, of which GSE90496 and GSE109379 were used as the training set and the validation set, respectively, and the remaining 11 sets were used as the independent test set. The random forest algorithm was used to select the CpG sites based on the importance of the features and a multilayer perceptron (MLP) model was trained to classify the samples. Deconvolution with the debCAM package was used to explore the cellular composition difference among tumors.Results: From training datasets with 2,801 samples, 396,568 CpG sites were retained after preprocessing, of which 767 were selected as the modeling features. A three-layer MLP model was developed, which consists of 1,320 nodes in the hidden layer, to predict the histological types of brain tumors. The prediction accuracy is 99.2, 87.0, and 96.58%, respectively, on the training, validation and test sets. The results of deconvolution analysis showed that the cell proportions of different tumor subtypes were different, and it is approximately enough to distinguish different tumor entities.Conclusion: We developed a classifier that is robust for the classification of central nervous system tumors, and tried to analyze the reasons for the classification performance.
format	article
author	Yuxing Chen Yixin Yan Moping Xu Wen Chen Jinyu Lin Yan Zhao Junze Wu Xianlong Wang Xianlong Wang
author_facet	Yuxing Chen Yixin Yan Moping Xu Wen Chen Jinyu Lin Yan Zhao Junze Wu Xianlong Wang Xianlong Wang
author_sort	Yuxing Chen
title	Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile
title_short	Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile
title_full	Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile
title_fullStr	Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile
title_full_unstemmed	Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile
title_sort	development of a machine learning classifier for brain tumors diagnosis based on dna methylation profile
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/0d848c47df394e3783d6250f30cce2ca
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_version_	1718442971494350848

Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile

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