ISSN: 2161-0681

Journal of Clinical & Experimental Pathology
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  • Research Article   
  • J Clin Exp Pathol 2017, Vol 8(1): 333
  • DOI: 10.4172/2161-0681.1000333

Application of a Blood-based Dynamic Genome Signature: How MAS5/RMA/PLIER Normalization Batches Affect Measured Gene Expression Profiling Stability in Clinical Diagnosis

Jonah Chao1, Gerald Chaban1, Changming Cheng2, Sanggetha Piarar3, C. C. Liew1,4,6* and Samuel Chao5
1Department of Laboratory Medicine and Pathobiology, Canada-China Healthcare Institute, , Ontario, Canada
2Department of Laboratory Medicine and Pathobiology, Shanghai Biochip Company Limited, , Shanghai, China
3Department of Laboratory Medicine and Pathobiology, Bionexus Gene Laboratory, University Sains Malaysia, Penang, Malaysia
4Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
5Department of Laboratory Medicine and Pathobiology, , ChaoSimulations, Ontario, Canada
6Department of Medicine, Brigham and Woman’s Hospital, Harvard Medical School, , Boston, Massachusetts, United States
*Corresponding Author : C. C. Liew, Canada-China Healthcare Institute, 351 Ferrier Street, Markham, L3R 5Z2, Ontario, United States, Tel: 647-929-4371, Email: cliew@cchi.com

Received Date: Dec 18, 2017 / Accepted Date: Jan 08, 2018 / Published Date: Jan 10, 2018

Abstract

Objective: A number of studies compare the microarray normalization methods MAS5 (Microarray Suite Version 5), RMA (Robust Multi-array Average) and PLIER (Probe Logarithmic Error Intensity Estimate) with respect to the rate at which genes of interest are identified. Here we evaluate and compare the stability of the measured gene expression when identical or technical replicate arrays are analyzed in batches of differing sizes and composition. These variations in measured gene expression have implications for clinical applications, which have requirements that differ significantly from those of research applications.
Methods: We evaluated the samples from data set E-MTAB-1532, available on ArrayExpress, a public repository of microarray data using the MAS5, RMA, and PLIER methods. We then evaluated a sample run as triplicate arrays and compared results among the different normalization methods.
Results and conclusion: Our study found that for some applications MAS5 is superior to the other methods, although the MAQC (Micro Array Quality Control) project, which extensively evaluated the performance of the platforms, reached a different conclusion.

Keywords: Microarray normalization methods; Microarray suite version; Robust multi-array average; Probe logarithmic error intensity estimate; Microarray; Gene expression; Microarray quality control project

Citation: Chao J, Chaban G, Cheng C, Piarar S, Liew CC, et al. (2018) Application of a Blood-based Dynamic Genome Signature: How MAS5/RMA/PLIER Normalization Batches Affect Measured Gene Expression Profiling Stability in Clinical Diagnosis. J Clin Exp Pathol 8: 333. Doi: 10.4172/2161-0681.1000333

Copyright: ©2017 Chao J, et al. 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 credited.

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