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Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis

BACKGROUND: Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. METHODOLOGY/PRINCIPAL FINDINGS: Human peripheral blood samples were drawn from h...

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Autores principales: Xu, Qinghua, Ni, Shujuan, Wu, Fei, Liu, Fang, Ye, Xun, Mougin, Bruno, Meng, Xia, Du, Xiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203156/
https://www.ncbi.nlm.nih.gov/pubmed/22046403
http://dx.doi.org/10.1371/journal.pone.0026905
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author Xu, Qinghua
Ni, Shujuan
Wu, Fei
Liu, Fang
Ye, Xun
Mougin, Bruno
Meng, Xia
Du, Xiang
author_facet Xu, Qinghua
Ni, Shujuan
Wu, Fei
Liu, Fang
Ye, Xun
Mougin, Bruno
Meng, Xia
Du, Xiang
author_sort Xu, Qinghua
collection PubMed
description BACKGROUND: Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. METHODOLOGY/PRINCIPAL FINDINGS: Human peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R (2) methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes). The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%), the significant impact of RNA quality on the expression of individual genes was observed. CONCLUSIONS: By characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study.
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spelling pubmed-32031562011-11-01 Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis Xu, Qinghua Ni, Shujuan Wu, Fei Liu, Fang Ye, Xun Mougin, Bruno Meng, Xia Du, Xiang PLoS One Research Article BACKGROUND: Human peripheral blood is a promising material for biomedical research. However, various kinds of biological and technological factors result in a large degree of variation in blood gene expression profiles. METHODOLOGY/PRINCIPAL FINDINGS: Human peripheral blood samples were drawn from healthy volunteers and analysed using the Human Genome U133Plus2 Microarray. We applied a novel approach using the Principle Component Analysis and Eigen-R (2) methods to dissect the overall variation of blood gene expression profiles with respect to the interested biological and technological factors. The results indicated that the predominating sources of the variation could be traced to the individual heterogeneity of the relative proportions of different blood cell types (leukocyte subsets and erythrocytes). The physiological factors like age, gender and BMI were demonstrated to be associated with 5.3% to 9.2% of the total variation in the blood gene expression profiles. We investigated the gene expression profiles of samples from the same donors but with different levels of RNA quality. Although the proportion of variation associated to the RNA Integrity Number was mild (2.1%), the significant impact of RNA quality on the expression of individual genes was observed. CONCLUSIONS: By characterizing the major sources of variation in blood gene expression profiles, such variability can be minimized by modifications to study designs. Increasing sample size, balancing confounding factors between study groups, using rigorous selection criteria for sample quality, and well controlled experimental processes will significantly improve the accuracy and reproducibility of blood transcriptome study. Public Library of Science 2011-10-27 /pmc/articles/PMC3203156/ /pubmed/22046403 http://dx.doi.org/10.1371/journal.pone.0026905 Text en Xu et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Xu, Qinghua
Ni, Shujuan
Wu, Fei
Liu, Fang
Ye, Xun
Mougin, Bruno
Meng, Xia
Du, Xiang
Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis
title Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis
title_full Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis
title_fullStr Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis
title_full_unstemmed Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis
title_short Investigation of Variation in Gene Expression Profiling of Human Blood by Extended Principle Component Analysis
title_sort investigation of variation in gene expression profiling of human blood by extended principle component analysis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203156/
https://www.ncbi.nlm.nih.gov/pubmed/22046403
http://dx.doi.org/10.1371/journal.pone.0026905
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